From bonnalraoul at ingm.it  Tue Mar  1 05:03:18 2011
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Tue, 1 Mar 2011 11:03:18 +0100
Subject: [Open-bio-l] [NGS] Design, Normalization, DiffExpression
Message-ID: <9C59CA8E-8B0A-4DB8-B9E2-88E6113D241E@ingm.it>


http://www.silencejournal.com/content/2/1/2/abstract

--
Ra

linkedin: http://it.linkedin.com/in/raoulbonnal
twitter: http://twitter.com/ilpuccio
skype: ilpuccio
irc.freenode.net: Helius
github: https://github.com/helios







From biopython at maubp.freeserve.co.uk  Thu Mar  3 08:17:39 2011
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 3 Mar 2011 13:17:39 +0000
Subject: [Open-bio-l] Moving from Bugzilla to Redmine on a cloud server
Message-ID: <AANLkTi=NRYHCrzsn6uttQyGdPGNtrX4YDEqGRvQn0k=p@mail.gmail.com>

Hi all,

This is a continuation of discussions on root-l and also on biojava-dev about
the Bio* project's bug tracker, which currently uses Bugzilla running on an
OBF hosted machine - http://bugzilla.open-bio.org/

http://lists.open-bio.org/pipermail/biojava-dev/2011-March/004582.html

Chris and Jason have been looking at using Redmine running on the Amazon
cloud, in part to simplify OBF server maintainance, and how to migrate the
Bugzilla data over to this.

Note that the open-bio-l mailing list archive is public, so keep that in mind
regarding passwords etc. See:

http://lists.open-bio.org/pipermail/open-bio-l/

Peter

---------- Forwarded message ----------
From: Peter <biopython at maubp.freeserve.co.uk>
Date: Thu, Mar 3, 2011 at 1:11 PM
Subject: Re: [Biojava-dev] Open bugs.
To: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>
Cc: Jason Stajich <jason.stajich at gmail.com>, Chris Dagdigian <chris at bioteam.net>


On Wed, Mar 2, 2011 at 2:23 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
> Thanks, Peter. As far as I know none of us is on the root-l, however a while ago
> Scooter and I suggested to get redmine installed on a vm on the support list. I
> was already wondering about the status of this since we never heard back....
> Can you give us a status update of this discussion?

There was some discussion on root-l (usually used for sys-admin stuff) with
Andreas etc CC'd. The root-l list is private (with no public archive) as often
general sensitive server details (e.g. host names, port numbers, and access
credentials) are discussed. However, I think there was broad agreement
that most of the RedMine discussion could happen in the open, probably
on the Open-Bio-l list. Anyone interested sign up here:
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Meanwhile, Chris has been blogging about some of his experiences:
http://blog.bioteam.net/2011/02/amazon-cloudformation-first-look/
http://blog.bioteam.net/2011/03/amazon-cloudformation-second-look/

Peter

From p.j.a.cock at googlemail.com  Fri Mar  4 06:45:11 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 11:45:11 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
Message-ID: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>

Hi all,

I've retitled this thread to reflect the current topic, and CC'd the open-bio-l
mailing list as Raoul suggested. Can we continue the discussion there?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>
>> Dear All,
>> a) this discussion is a good starting point for a workgroup during Codefest
>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>> testing our projects ?! It would be fun to see all the bio* with stats about
>> testing etc...
>
> I think the buildbot instance covers some of that, but they are mainly
> automated builds:
>
> http://testing.open-bio.org/
>
> biopython is the only one set up currently.

Note that this is a small Amazon cloud machine, and doesn't actually run
the tests itself (that would require a more expensive machine due to the
higher load). Instead we need client machines (covering a range of OS,
Python version etc) whose run-time is donated (currently by Biopython
developers or their employers).

When setting up http://testing.open-bio.org/ the intention was to have
it host other Bio* projects too - and they don't have to be using the
buildbot software (but they could if they wanted to).

>> b) testing is very important and new contributes should be accepted
>> only with tests, which implies a problem how to check fake tests? :-)
>
> Code review and checking the test results. ?Otherwise, you have to trust
> your developers.

This is something we're pushing much more with Biopython in recent
years (a depressing amount of legacy code had no tests when I first
got involved, things are a lot better now). For any new code contributions
we do ask for tests and minimal documentation (and try and work
with the contributor to help this happen).

>> c) usually ruby's community relies a lot on doc==tests that's
>> completely wrong, because the newbies can't read fluently the
>> code, also because there are different tools and sometimes a lot
>> of mocking.

With Biopython we're starting to make more use of testable docs
(Python's doctest system) which is really good I think. But you are
right, you need proper unit tests AS WELL. With our doctests,
the primary aim is to be useful documentation (which can double
as a basic functional test).

>> c.a) recently i had an idea, but I have no time to do that: establish
>> a relationship between a mock and a real object and validate the
>> mock or enable it only if the real object has been tested before.
>> That would make mocking more sens to me, but i think this is
>> another story.
>
> Yes, I've thought about that as well re: Moose-based work, haven't
> wrapped my head around it either.

I'm not quite following - it may be a terminology difference.

>> d) I agree with Toshiaki, after this very useful brain storming
>> start working (Impressed to see all this traffic :-) )
>>
>> Cheers.
>
> +1. ?Will be interesting to see how things progress.
>
> chris

Same here :)

Peter


From p.j.a.cock at googlemail.com  Fri Mar  4 07:23:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 12:23:53 +0000
Subject: [Open-bio-l] Automated testing server for BioJava?
Message-ID: <AANLkTi=+6Z9hHNpwsNeK48V63yQO7yf9MMim5ds3+q8u@mail.gmail.com>

Hi all,

Just FYI, the OBF have a new (Amazon cloud) server running at
http://testing.open-bio.org which we are currently using to host
a buildbot for Biopython. Currently Tiago and I (from Biopython)
have been tinkering with this with help from Chris Dagdigian
on the sys-admin/cloud side.

The idea is that similar services could be setup for the other
Bio* projects (using buildbot or some other software), if you
are interested.

Note that this is a low power server and it is not intended to
be used to run tests itself - that is a job for separate build
slave machines (which should cover a range of OS,
python/java/perl/ruby versions etc).

For further discussion, can I point you here:
http://lists.open-bio.org/pipermail/open-bio-l/2011-March/000743.html

See also this BioRuby thread:
http://lists.open-bio.org/pipermail/bioruby/2011-March/001720.html
http://lists.open-bio.org/pipermail/bioruby/2011-March/001734.html

Regards,

Peter

From chapmanb at 50mail.com  Fri Mar  4 07:36:44 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 4 Mar 2011 07:36:44 -0500
Subject: [Open-bio-l] Bioinformatics Open Source Conference (BOSC
 2011)--Call for Abstracts
Message-ID: <20110304123644.GB27839@sobchak>

We invite you to submit an abstract to BOSC 2011! Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration". We
are also working to arrange a joint session with one of the other ISMB
SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student Travel
Awards for BOSC 2011. Each winner will be awarded $250 to defray the
costs of travel to BOSC 2011.
 
For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor 

From cjfields at illinois.edu  Fri Mar  4 09:14:12 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 08:14:12 -0600
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
Message-ID: <06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>

On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:

> Hi all,
> 
> I've retitled this thread to reflect the current topic, and CC'd the open-bio-l
> mailing list as Raoul suggested. Can we continue the discussion there?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l

Agreed.  I'm replying only on open-bio-l to promote that.

> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>> 
>>> Dear All,
>>> a) this discussion is a good starting point for a workgroup during Codefest
>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>> testing etc...
>> 
>> I think the buildbot instance covers some of that, but they are mainly
>> automated builds:
>> 
>> http://testing.open-bio.org/
>> 
>> biopython is the only one set up currently.
> 
> Note that this is a small Amazon cloud machine, and doesn't actually run
> the tests itself (that would require a more expensive machine due to the
> higher load). Instead we need client machines (covering a range of OS,
> Python version etc) whose run-time is donated (currently by Biopython
> developers or their employers).
> 
> When setting up http://testing.open-bio.org/ the intention was to have
> it host other Bio* projects too - and they don't have to be using the
> buildbot software (but they could if they wanted to).

I think it would be nice to have a smoke server there as well (I don't think buildbot can do that, AFAIK).  Will ask Chris D about it.

I like the fact that we now are diversifying beyond perl-based solutions with buildbot and redmine (I would include mediawiki, but PHP gives me the hives :).  Any easily-installable Java-based ones?

>>> b) testing is very important and new contributes should be accepted
>>> only with tests, which implies a problem how to check fake tests? :-)
>> 
>> Code review and checking the test results.  Otherwise, you have to trust
>> your developers.
> 
> This is something we're pushing much more with Biopython in recent
> years (a depressing amount of legacy code had no tests when I first
> got involved, things are a lot better now). For any new code contributions
> we do ask for tests and minimal documentation (and try and work
> with the contributor to help this happen).

Same here.  This is a common cycle with OS projects.

>>> c) usually ruby's community relies a lot on doc==tests that's
>>> completely wrong, because the newbies can't read fluently the
>>> code, also because there are different tools and sometimes a lot
>>> of mocking.
> 
> With Biopython we're starting to make more use of testable docs
> (Python's doctest system) which is really good I think. But you are
> right, you need proper unit tests AS WELL. With our doctests,
> the primary aim is to be useful documentation (which can double
> as a basic functional test).

The problem with bioperl is that much of the testing framework for in-line or testable docs wasn't present during the initial development process.  We also have a LOT of cruft modules that lack true author support. 

What we are planning on for future releases is to modularize bioperl installations, with an installer to put together the dists one wants.  The current release has well over 1000 classes and modules; modularizing will help remove some of the maintenance headaches we had been facing during development.  We are also pushing new code to go into separate CPAN installations, as these can be added to an installer as needed (as someone else long ago put it, we're essentially creating a mini-BioPerlPAN within CPAN).

>>> c.a) recently i had an idea, but I have no time to do that: establish
>>> a relationship between a mock and a real object and validate the
>>> mock or enable it only if the real object has been tested before.
>>> That would make mocking more sens to me, but i think this is
>>> another story.
>> 
>> Yes, I've thought about that as well re: Moose-based work, haven't
>> wrapped my head around it either.
> 
> I'm not quite following - it may be a terminology difference.

Perl thing; Moose makes tests using mocked objects a bit easier.  I have a side project that re-implements bioperl classes using Moose, has had some pretty promising results.

chris

>>> d) I agree with Toshiaki, after this very useful brain storming
>>> start working (Impressed to see all this traffic :-) )
>>> 
>>> Cheers.
>> 
>> +1.  Will be interesting to see how things progress.
>> 
>> chris
> 
> Same here :)
> 
> Peter



From p.j.a.cock at googlemail.com  Fri Mar  4 10:04:36 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 15:04:36 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
Message-ID: <AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>

On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>
>>>> Dear All,
>>>> a) this discussion is a good starting point for a workgroup during Codefest
>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>>> testing etc...
>>>
>>> I think the buildbot instance covers some of that, but they are mainly
>>> automated builds:
>>>
>>> http://testing.open-bio.org/
>>>
>>> biopython is the only one set up currently.
>>
>> Note that this is a small Amazon cloud machine, and doesn't actually run
>> the tests itself (that would require a more expensive machine due to the
>> higher load). Instead we need client machines (covering a range of OS,
>> Python version etc) whose run-time is donated (currently by Biopython
>> developers or their employers).
>>
>> When setting up http://testing.open-bio.org/ the intention was to have
>> it host other Bio* projects too - and they don't have to be using the
>> buildbot software (but they could if they wanted to).
>
> I think it would be nice to have a smoke server there as well (I don't
> think buildbot can do that, AFAIK). ?Will ask Chris D about it.

Can you clarify what you mean by smoke server? I'd assumed it was
a product name but now it sounds like you mean some methodology.

We have buildbot setup to do a nightly test of the latest code on all
the slaves. Additionally, via the web interface an admin can force a
rebuild, and force a build of the current latest code.

In theory one can also hook up buildbot to run tests triggered by
commits - I understand this isn't available for git repositories yet
though (at least, that's my recollection from dicussion with Tiago,
BCC'd in case he isn't on open-bio-l yet).

> I like the fact that we now are diversifying beyond perl-based
> solutions with buildbot and redmine (I would include mediawiki,
> but PHP gives me the hives :). ?Any easily-installable Java-based
> ones?

As long as the OBF has enough people familiar with the tool
to support it, I don't care what language it is written in.

>>>> b) testing is very important and new contributes should be accepted
>>>> only with tests, which implies a problem how to check fake tests? :-)
>>>
>>> Code review and checking the test results. ?Otherwise, you have to trust
>>> your developers.
>>
>> This is something we're pushing much more with Biopython in recent
>> years (a depressing amount of legacy code had no tests when I first
>> got involved, things are a lot better now). For any new code contributions
>> we do ask for tests and minimal documentation (and try and work
>> with the contributor to help this happen).
>
> Same here. ?This is a common cycle with OS projects.
>
>>>> c) usually ruby's community relies a lot on doc==tests that's
>>>> completely wrong, because the newbies can't read fluently the
>>>> code, also because there are different tools and sometimes a lot
>>>> of mocking.
>>
>> With Biopython we're starting to make more use of testable docs
>> (Python's doctest system) which is really good I think. But you are
>> right, you need proper unit tests AS WELL. With our doctests,
>> the primary aim is to be useful documentation (which can double
>> as a basic functional test).
>
> The problem with bioperl is that much of the testing framework
> for in-line or testable docs wasn't present during the initial
> development process. ?We also have a LOT of cruft modules
> that lack true author support.

Also true for Biopython to some extent.

> What we are planning on for future releases is to modularize
> bioperl installations, with an installer to put together the dists
> one wants. ?The current release has well over 1000 classes
> and modules; modularizing will help remove some of the
> maintenance headaches we had been facing during
> development. ?We are also pushing new code to go into
> separate CPAN installations, as these can be added to an
> installer as needed (as someone else long ago put it, we're
> essentially creating a mini-BioPerlPAN within CPAN).

I'm happy enough with the current Biopython monolith install -
although we are slowly gaining extra runtime dependencies,
doing the install/build is pretty easy. As the Python packaging
infrastructure matures, we too may want to consider
modularising - but for now I feel that is premature.

There is also an issue here for testing - if you can have a
diverse set of build slaves, then hopefully some will have
and some will lack each soft dependency. This is useful to
check graceful failure when things are missing.

Peter


From cjfields at illinois.edu  Fri Mar  4 10:58:01 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 09:58:01 -0600
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
Message-ID: <095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>

On Mar 4, 2011, at 9:04 AM, Peter Cock wrote:

> On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>> 
>>>>> Dear All,
>>>>> a) this discussion is a good starting point for a workgroup during Codefest
>>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>>>> testing etc...
>>>> 
>>>> I think the buildbot instance covers some of that, but they are mainly
>>>> automated builds:
>>>> 
>>>> http://testing.open-bio.org/
>>>> 
>>>> biopython is the only one set up currently.
>>> 
>>> Note that this is a small Amazon cloud machine, and doesn't actually run
>>> the tests itself (that would require a more expensive machine due to the
>>> higher load). Instead we need client machines (covering a range of OS,
>>> Python version etc) whose run-time is donated (currently by Biopython
>>> developers or their employers).
>>> 
>>> When setting up http://testing.open-bio.org/ the intention was to have
>>> it host other Bio* projects too - and they don't have to be using the
>>> buildbot software (but they could if they wanted to).
>> 
>> I think it would be nice to have a smoke server there as well (I don't
>> think buildbot can do that, AFAIK).  Will ask Chris D about it.
> 
> Can you clarify what you mean by smoke server? I'd assumed it was
> a product name but now it sounds like you mean some methodology.
> 
> We have buildbot setup to do a nightly test of the latest code on all
> the slaves. Additionally, via the web interface an admin can force a
> rebuild, and force a build of the current latest code.
> 
> In theory one can also hook up buildbot to run tests triggered by
> commits - I understand this isn't available for git repositories yet
> though (at least, that's my recollection from dicussion with Tiago,
> BCC'd in case he isn't on open-bio-l yet).

A smoke server holds test results submitted from users, or really anyone who has a set of modules/tools installed; it can be part of the build/testing process.  It's less automated building and more distributed than buildbot: the server doesn't call out to a specific set of build servers to run builds and tests, but relies on the community (developers, users) to run tests and submit them.  CPAN has this built in via CPAN Testers; one can install a set of modules and then, every time a dist is installed via CPAN a test report is sent to a remote server:

http://www.cpantesters.org/distro/B/bioperl.html

This is similar to what the bioruby folks are searching for, if I'm not mistaken.  

(Just so there is no confusion, in most cases with software 'smoke testing' refers to a set of prelim tests to make sure a build works, but in practice with small projects the term equally applies to running every test)

>> I like the fact that we now are diversifying beyond perl-based
>> solutions with buildbot and redmine (I would include mediawiki,
>> but PHP gives me the hives :).  Any easily-installable Java-based
>> ones?
> 
> As long as the OBF has enough people familiar with the tool
> to support it, I don't care what language it is written in.

Same here.

chris




From andreas at sdsc.edu  Fri Mar  4 11:34:39 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Mar 2011 08:34:39 -0800
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
Message-ID: <AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>

Just to quickly add, for BioJava, we are already using CruiseControl
for automated testing, building and making nightly releases. I am
hosting this on one of my work servers:
http://source.rcsb.org:8080/cruisecontrol/  but would be happy if this
would be moved to an OBF service.

Only issue with this system is that mailman keeps filtering out the
notification emails that are being generated if one of the junit tests
(or compilation) fails, so I still have to myself keep chasing
developers who break the build.

Andreas

On Fri, Mar 4, 2011 at 7:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 4, 2011, at 9:04 AM, Peter Cock wrote:
>
>> On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>>>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>>>
>>>>>> Dear All,
>>>>>> a) this discussion is a good starting point for a workgroup during Codefest
>>>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>>>>> testing etc...
>>>>>
>>>>> I think the buildbot instance covers some of that, but they are mainly
>>>>> automated builds:
>>>>>
>>>>> http://testing.open-bio.org/
>>>>>
>>>>> biopython is the only one set up currently.
>>>>
>>>> Note that this is a small Amazon cloud machine, and doesn't actually run
>>>> the tests itself (that would require a more expensive machine due to the
>>>> higher load). Instead we need client machines (covering a range of OS,
>>>> Python version etc) whose run-time is donated (currently by Biopython
>>>> developers or their employers).
>>>>
>>>> When setting up http://testing.open-bio.org/ the intention was to have
>>>> it host other Bio* projects too - and they don't have to be using the
>>>> buildbot software (but they could if they wanted to).
>>>
>>> I think it would be nice to have a smoke server there as well (I don't
>>> think buildbot can do that, AFAIK). ?Will ask Chris D about it.
>>
>> Can you clarify what you mean by smoke server? I'd assumed it was
>> a product name but now it sounds like you mean some methodology.
>>
>> We have buildbot setup to do a nightly test of the latest code on all
>> the slaves. Additionally, via the web interface an admin can force a
>> rebuild, and force a build of the current latest code.
>>
>> In theory one can also hook up buildbot to run tests triggered by
>> commits - I understand this isn't available for git repositories yet
>> though (at least, that's my recollection from dicussion with Tiago,
>> BCC'd in case he isn't on open-bio-l yet).
>
> A smoke server holds test results submitted from users, or really anyone who has a set of modules/tools installed; it can be part of the build/testing process. ?It's less automated building and more distributed than buildbot: the server doesn't call out to a specific set of build servers to run builds and tests, but relies on the community (developers, users) to run tests and submit them. ?CPAN has this built in via CPAN Testers; one can install a set of modules and then, every time a dist is installed via CPAN a test report is sent to a remote server:
>
> http://www.cpantesters.org/distro/B/bioperl.html
>
> This is similar to what the bioruby folks are searching for, if I'm not mistaken.
>
> (Just so there is no confusion, in most cases with software 'smoke testing' refers to a set of prelim tests to make sure a build works, but in practice with small projects the term equally applies to running every test)
>
>>> I like the fact that we now are diversifying beyond perl-based
>>> solutions with buildbot and redmine (I would include mediawiki,
>>> but PHP gives me the hives :). ?Any easily-installable Java-based
>>> ones?
>>
>> As long as the OBF has enough people familiar with the tool
>> to support it, I don't care what language it is written in.
>
> Same here.
>
> chris
>
>
>
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From p.j.a.cock at googlemail.com  Fri Mar  4 11:45:32 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 16:45:32 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
Message-ID: <AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>

On Fri, Mar 4, 2011 at 4:34 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Just to quickly add, for BioJava, we are already using CruiseControl
> for automated testing, building and making nightly releases. I am
> hosting this on one of my work servers:
> http://source.rcsb.org:8080/cruisecontrol/ ?but would be happy if this
> would be moved to an OBF service.

I see, from http://cruisecontrol.sourceforge.net/

Would you be happy with http://testing.open-bio.org/biojava/ as the URL?

Are there any gotchas with installing it? e.g. dependencies? I guess
you'll need to contact Chris D to get access to the machine and
also sign up to root-l to keep you in the loop with any sys admin.
He'll probably want to know things like expected machine load
(e.g. is it RAM hungry?).

> Only issue with this system is that mailman keeps filtering out the
> notification emails that are being generated if one of the junit tests
> (or compilation) fails, so I still have to myself keep chasing
> developers who break the build.

So far I'm getting buildbot emails from testing.open-bio.org so
you may find it works OK from the new location.

Peter


From andreas at sdsc.edu  Fri Mar  4 11:59:15 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Mar 2011 08:59:15 -0800
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
Message-ID: <AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>

> I see, from http://cruisecontrol.sourceforge.net/

correct

> Would you be happy with http://testing.open-bio.org/biojava/ as the URL?

sure

> Are there any gotchas with installing it?

it is all in Java and requires also a Tomcat server running on one
port. There was something about not having too much CPU available on
the VM? Some of the junit tests in biojava require a bit of CPU. RAM
requirement currently is < 512M and finally SSH keys have to be set up
so the build system can upload the latest biojava snapshots to the
Maven build archive...


> So far I'm getting buildbot emails from testing.open-bio.org so
> you may find it works OK from the new location.

problem is not the sending of the mails but getting them accepted on
biojava-l and -dev. They keep getting flagged as suspicious mails due
to the long HTML content.

Andreas

>
> Peter
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------

From p.j.a.cock at googlemail.com  Fri Mar  4 12:08:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 17:08:58 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
Message-ID: <AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>

On Fri, Mar 4, 2011 at 4:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> I see, from http://cruisecontrol.sourceforge.net/
>
> correct
>
>> Would you be happy with http://testing.open-bio.org/biojava/ as the URL?
>
> sure
>
>> Are there any gotchas with installing it?
>
> it is all in Java and requires also a Tomcat server running on one
> port. There was something about not having too much CPU available on
> the VM? Some of the junit tests in biojava require a bit of CPU. RAM
> requirement currently is < 512M and finally SSH keys have to be set up
> so the build system can upload the latest biojava snapshots to the
> Maven build archive...

You mean it runs the unit tests itself? Hmm - that may not fit with
type of Amazon machine Chris D is renting for testing.open-bio.org
(buildbot doesn't do any heavy lifting - a separate pool of slaves
run the unit tests).

>> So far I'm getting buildbot emails from testing.open-bio.org so
>> you may find it works OK from the new location.
>
> problem is not the sending of the mails but getting them accepted on
> biojava-l and -dev. They keep getting flagged as suspicious mails due
> to the long HTML content.

OK - I assumed it would be down to the sender's DNS or something.
As you say, long HTML content is a different issue.

Peter

From andreas at sdsc.edu  Fri Mar  4 12:14:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Mar 2011 09:14:57 -0800
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
	<AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>
Message-ID: <AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>

> You mean it runs the unit tests itself? Hmm - that may not fit with
> type of Amazon machine Chris D is renting for testing.open-bio.org
> (buildbot doesn't do any heavy lifting - a separate pool of slaves
> run the unit tests).

Yes, running junit tests is part of the Maven release process. (you
can only make a release if the code compiles and all tests are
passed). Since Java is coming with its own VM, we don't need to test
on all possible architectures. Considering this, perhaps it would be
sufficient to redirect http://testing.open-bio.org/biojava/ to
http://source.rcsb.org:8080/cruisecontrol/  ...

Andreas

From p.j.a.cock at googlemail.com  Fri Mar  4 12:20:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 17:20:53 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
	<AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>
	<AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
Message-ID: <AANLkTim_V6K0zBXc7kMSBei_cTDuW_mj9YrM4XsvBjp4@mail.gmail.com>

On Fri, Mar 4, 2011 at 5:14 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> You mean it runs the unit tests itself? Hmm - that may not fit with
>> type of Amazon machine Chris D is renting for testing.open-bio.org
>> (buildbot doesn't do any heavy lifting - a separate pool of slaves
>> run the unit tests).
>
> Yes, running junit tests is part of the Maven release process. (you
> can only make a release if the code compiles and all tests are
> passed). Since Java is coming with its own VM, we don't need to test
> on all possible architectures. Considering this, perhaps it would be
> sufficient to redirect http://testing.open-bio.org/biojava/ to
> http://source.rcsb.org:8080/cruisecontrol/ ?...

That sounds like a practical short term solution :)

Let's give Chris D a chance to comment though.

Peter


From heuermh at acm.org  Fri Mar  4 16:09:13 2011
From: heuermh at acm.org (Michael Heuer)
Date: Fri, 4 Mar 2011 16:09:13 -0500 (EST)
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.1103041557020.16914-100000@shell3.shore.net>

On Fri, 4 Mar 2011, Andreas Prlic wrote:

> > You mean it runs the unit tests itself? Hmm - that may not fit with
> > type of Amazon machine Chris D is renting for testing.open-bio.org
> > (buildbot doesn't do any heavy lifting - a separate pool of slaves
> > run the unit tests).
>
> Yes, running junit tests is part of the Maven release process. (you
> can only make a release if the code compiles and all tests are
> passed). Since Java is coming with its own VM, we don't need to test
> on all possible architectures. Considering this, perhaps it would be
> sufficient to redirect http://testing.open-bio.org/biojava/ to
> http://source.rcsb.org:8080/cruisecontrol/  ...

Hello Andreas,

Hudson/Jenkins/Nectar/whatever you want to call it has support for build
slave instances, with Amazon EC2 cloud support and such.  Perhaps it might
be possible to set it up on testing.open-bio.org and farm out to rcsb.org
and/or other sites.

http://cloudbees.com
http://nectar.cloudbees.com
http://jenkins-ci.org
http://hudson-ci.org

   michael


From tiagoantao at gmail.com  Fri Mar  4 10:36:57 2011
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Fri, 4 Mar 2011 15:36:57 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
Message-ID: <AANLkTikJBhXANjgyESy8NSj5Zhj3V5X-iKpNrC_ozok0@mail.gmail.com>

On mobile phone, fast mail. Buidbot CAN be trigerred by git commits.

2011/3/4, Peter Cock <p.j.a.cock at googlemail.com>:
> On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu>
>>> wrote:
>>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>>
>>>>> Dear All,
>>>>> a) this discussion is a good starting point for a workgroup during
>>>>> Codefest
>>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the
>>>>> addr
>>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>>> testing our projects ?! It would be fun to see all the bio* with stats
>>>>> about
>>>>> testing etc...
>>>>
>>>> I think the buildbot instance covers some of that, but they are mainly
>>>> automated builds:
>>>>
>>>> http://testing.open-bio.org/
>>>>
>>>> biopython is the only one set up currently.
>>>
>>> Note that this is a small Amazon cloud machine, and doesn't actually run
>>> the tests itself (that would require a more expensive machine due to the
>>> higher load). Instead we need client machines (covering a range of OS,
>>> Python version etc) whose run-time is donated (currently by Biopython
>>> developers or their employers).
>>>
>>> When setting up http://testing.open-bio.org/ the intention was to have
>>> it host other Bio* projects too - and they don't have to be using the
>>> buildbot software (but they could if they wanted to).
>>
>> I think it would be nice to have a smoke server there as well (I don't
>> think buildbot can do that, AFAIK). ?Will ask Chris D about it.
>
> Can you clarify what you mean by smoke server? I'd assumed it was
> a product name but now it sounds like you mean some methodology.
>
> We have buildbot setup to do a nightly test of the latest code on all
> the slaves. Additionally, via the web interface an admin can force a
> rebuild, and force a build of the current latest code.
>
> In theory one can also hook up buildbot to run tests triggered by
> commits - I understand this isn't available for git repositories yet
> though (at least, that's my recollection from dicussion with Tiago,
> BCC'd in case he isn't on open-bio-l yet).
>
>> I like the fact that we now are diversifying beyond perl-based
>> solutions with buildbot and redmine (I would include mediawiki,
>> but PHP gives me the hives :). ?Any easily-installable Java-based
>> ones?
>
> As long as the OBF has enough people familiar with the tool
> to support it, I don't care what language it is written in.
>
>>>>> b) testing is very important and new contributes should be accepted
>>>>> only with tests, which implies a problem how to check fake tests? :-)
>>>>
>>>> Code review and checking the test results. ?Otherwise, you have to trust
>>>> your developers.
>>>
>>> This is something we're pushing much more with Biopython in recent
>>> years (a depressing amount of legacy code had no tests when I first
>>> got involved, things are a lot better now). For any new code
>>> contributions
>>> we do ask for tests and minimal documentation (and try and work
>>> with the contributor to help this happen).
>>
>> Same here. ?This is a common cycle with OS projects.
>>
>>>>> c) usually ruby's community relies a lot on doc==tests that's
>>>>> completely wrong, because the newbies can't read fluently the
>>>>> code, also because there are different tools and sometimes a lot
>>>>> of mocking.
>>>
>>> With Biopython we're starting to make more use of testable docs
>>> (Python's doctest system) which is really good I think. But you are
>>> right, you need proper unit tests AS WELL. With our doctests,
>>> the primary aim is to be useful documentation (which can double
>>> as a basic functional test).
>>
>> The problem with bioperl is that much of the testing framework
>> for in-line or testable docs wasn't present during the initial
>> development process. ?We also have a LOT of cruft modules
>> that lack true author support.
>
> Also true for Biopython to some extent.
>
>> What we are planning on for future releases is to modularize
>> bioperl installations, with an installer to put together the dists
>> one wants. ?The current release has well over 1000 classes
>> and modules; modularizing will help remove some of the
>> maintenance headaches we had been facing during
>> development. ?We are also pushing new code to go into
>> separate CPAN installations, as these can be added to an
>> installer as needed (as someone else long ago put it, we're
>> essentially creating a mini-BioPerlPAN within CPAN).
>
> I'm happy enough with the current Biopython monolith install -
> although we are slowly gaining extra runtime dependencies,
> doing the install/build is pretty easy. As the Python packaging
> infrastructure matures, we too may want to consider
> modularising - but for now I feel that is premature.
>
> There is also an issue here for testing - if you can have a
> diverse set of build slaves, then hopefully some will have
> and some will lack each soft dependency. This is useful to
> check graceful failure when things are missing.
>
> Peter
>

-- 
Enviada a partir do meu dispositivo m?vel

"If you want to get laid, go to college.  If you want an education, go
to the library." - Frank Zappa


From jason.stajich at gmail.com  Sat Mar  5 17:11:19 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 05 Mar 2011 14:11:19 -0800
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
Message-ID: <4D72B507.802@gmail.com>

This is probably also a message that would be helpful to generally get 
members from the various projects involved.

-------- Original Message --------
From: 	Hilmar Lapp <hlapp at drycafe.net>
Subject: 	[Root-l] Source Code page on OBF wiki
Date: 	Sat, 5 Mar 2011 13:59:49 -0500
To: 	Root-l <root-l at open-bio.org>



This page seems highly outdated: http://open-bio.org/wiki/SourceCode

I could take a stab at correcting some of the stuff, but don't even
have the complete picture necessary to fix it, so if someone who does
would do so that'd be great help. I'm also wondering to what extent we
should trim down the information here and link to the individual
project wikis instead.

I got here from the BioSQL wiki which links there for instructions on
obtaining source code through anonymous svn access. That doesn't apply
anymore, but there also is no section on anonymously obtaining code
through git. One question I'm asking myself is whether we even need to
document that, given that Github explains it already.

Anyone any thoughts on what we should focus on in this page?

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================




_______________________________________________
Root-l mailing list
Root-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/root-l


From jason.stajich at gmail.com  Sat Mar  5 17:25:10 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 05 Mar 2011 14:25:10 -0800
Subject: [Open-bio-l] held msgs
Message-ID: <4D72B846.5000605@gmail.com>

Sorry - there were some held messages from last summer that were never 
moderated. I've allowed them through but that will explain the blast 
from the past.

-- 
Jason Stajich



From hlapp at drycafe.net  Sat Mar  5 21:58:04 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Mar 2011 21:58:04 -0500
Subject: [Open-bio-l] Job opening for GMOD User Support Specialist
Message-ID: <814155D1-1CD5-4E66-B726-2CF7E33EF3CE@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities. If you know someone who might be  
interested please forward.)

============================
GMOD User Support Specialist
============================

Are you fascinated by genomics and bioinformatics? Are you passionate  
about collaborative open-source software? Do you enjoy teaching and  
working with scientists?  If so, then this position is for you.

The Generic Model Organism Database project (GMOD) is a collection of  
open source software tools for creating and managing biological, and  
particularly genomic, databases.  GMOD has a large, highly  
distributed, and dynamic community of software users and developers.   
The University of North Carolina at Chapel Hill has an opening for a  
GMOD user support specialist, to be based at the US National  
Evolutionary Synthesis Center (NESCent, www.nescent.org) in Durham,  
North Carolina, while serving the international community of GMOD users.

Job Description:

The GMOD user support specialist will maintain online documentation;  
respond to mailing list help requests; present tutorials; organize  
short courses, conference sessions and other community building  
activities; survey user needs, and recruit members of the community to  
assist with these functions.   The incumbent will collaborate closely  
with the GMOD Coordinator (Scott Cain, The Ontario Institute for  
Cancer Research) and other distributed personnel.  See http://gmod.org/wiki/GMOD_Help_Desk 
  for more background on the activities of the user support  
specialist.  The salary range is $68,906 to $82,687, depending on  
qualifications, and the incumbent will receive a comprehensive  
benefits package as an SPA employee within the UNC system.

Qualifications:

Required qualifications include: excellent written and verbal  
communication skills; team orientation with strong interpersonal  
skills. Preferred qualifications include: an MS or PhD in biology,  
computer science or related field; three or more years of experience  
with web programming and relational database management systems; three  
or more years of experience with genome database administration or  
curation, preferably in a GMOD environment; at least one year of  
experience with web content management, ideally using MediaWiki;  
freedom to travel 5-15 weeks/yr.

To Apply:

Please provide a cover letter and CV, including contact information  
for three references, to Hilmar Lapp, Assistant Director of  
Informatics, NESCent, at hlapp at nescent.org, and submit materials  
through http://bit.ly/h9l74r.  Inquiries may be addressed to H. Lapp  
by email or by phone at 919.668.5288.

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From dan.bolser at gmail.com  Sun Mar  6 15:57:32 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 6 Mar 2011 20:57:32 +0000
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <4D72B507.802@gmail.com>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
	<4D72B507.802@gmail.com>
Message-ID: <AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>

Does open bio really house all the code from all these bio projects? I
guess not...

If not, I'd turn this page into a table of links to the equivalent
pages for the other projects.

My own feeling is that when it comes to documentation, less is more
(or it should be as modular as possible). I hate it when GBrowse
starts telling me precisely how to install Apache and MySQL, but
apparently some people like it like that.


On 5 March 2011 22:11, Jason Stajich <jason.stajich at gmail.com> wrote:
> This is probably also a message that would be helpful to generally get
> members from the various projects involved.
>
> -------- Original Message --------
> From: ? Hilmar Lapp <hlapp at drycafe.net>
> Subject: ? ? ? ?[Root-l] Source Code page on OBF wiki
> Date: ? Sat, 5 Mar 2011 13:59:49 -0500
> To: ? ? Root-l <root-l at open-bio.org>
>
>
>
> This page seems highly outdated: http://open-bio.org/wiki/SourceCode
>
> I could take a stab at correcting some of the stuff, but don't even
> have the complete picture necessary to fix it, so if someone who does
> would do so that'd be great help. I'm also wondering to what extent we
> should trim down the information here and link to the individual
> project wikis instead.
>
> I got here from the BioSQL wiki which links there for instructions on
> obtaining source code through anonymous svn access. That doesn't apply
> anymore, but there also is no section on anonymously obtaining code
> through git. One question I'm asking myself is whether we even need to
> document that, given that Github explains it already.
>
> Anyone any thoughts on what we should focus on in this page?
>
> ? ? ? ?-hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
> _______________________________________________
> Root-l mailing list
> Root-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/root-l
>
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>


From cjfields at illinois.edu  Sun Mar  6 16:50:36 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 6 Mar 2011 15:50:36 -0600
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
	<4D72B507.802@gmail.com>
	<AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>
Message-ID: <14C9E6AB-8192-4941-972B-B5A601A37A74@illinois.edu>

On Mar 6, 2011, at 2:57 PM, Dan Bolser wrote:

> Does open bio really house all the code from all these bio projects? I
> guess not...

Depends on what you mean by 'house', all of these were present in open-bio version control (CVS/SVN) at one point, but most repos have recently migrated away from the open-bio-centric version control.  EMBOSS and a few others are still using CVS I think.

> If not, I'd turn this page into a table of links to the equivalent
> pages for the other projects.

Agreed.

> My own feeling is that when it comes to documentation, less is more
> (or it should be as modular as possible). I hate it when GBrowse
> starts telling me precisely how to install Apache and MySQL, but
> apparently some people like it like that.

GBrowse users are fairly diverse (ranging from users well-versed with SQL/Apache/etc and other not so much:).  I would rather have too much documentation, but have it be well-organized to the point where more experienced users can bypass certain instructions.

chris

> On 5 March 2011 22:11, Jason Stajich <jason.stajich at gmail.com> wrote:
>> This is probably also a message that would be helpful to generally get
>> members from the various projects involved.
>> 
>> -------- Original Message --------
>> From:   Hilmar Lapp <hlapp at drycafe.net>
>> Subject:        [Root-l] Source Code page on OBF wiki
>> Date:   Sat, 5 Mar 2011 13:59:49 -0500
>> To:     Root-l <root-l at open-bio.org>
>> 
>> 
>> 
>> This page seems highly outdated: http://open-bio.org/wiki/SourceCode
>> 
>> I could take a stab at correcting some of the stuff, but don't even
>> have the complete picture necessary to fix it, so if someone who does
>> would do so that'd be great help. I'm also wondering to what extent we
>> should trim down the information here and link to the individual
>> project wikis instead.
>> 
>> I got here from the BioSQL wiki which links there for instructions on
>> obtaining source code through anonymous svn access. That doesn't apply
>> anymore, but there also is no section on anonymously obtaining code
>> through git. One question I'm asking myself is whether we even need to
>> document that, given that Github explains it already.
>> 
>> Anyone any thoughts on what we should focus on in this page?
>> 
>>        -hilmar
>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Root-l mailing list
>> Root-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/root-l
>> 
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>> 
> 
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l



From dan.bolser at gmail.com  Mon Mar  7 04:21:19 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 7 Mar 2011 09:21:19 +0000
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <14C9E6AB-8192-4941-972B-B5A601A37A74@illinois.edu>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
	<4D72B507.802@gmail.com>
	<AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>
	<14C9E6AB-8192-4941-972B-B5A601A37A74@illinois.edu>
Message-ID: <AANLkTi=brtYKFV7E5Q+WnFVN6V_r2qUyqu4e2ZYqe9vw@mail.gmail.com>

On 6 March 2011 21:50, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 6, 2011, at 2:57 PM, Dan Bolser wrote:
>
>> Does open bio really house all the code from all these bio projects? I
>> guess not...
>
> Depends on what you mean by 'house', all of these were present in open-bio version control (CVS/SVN) at one point, but most repos have recently migrated away from the open-bio-centric version control. ?EMBOSS and a few others are still using CVS I think.
>
>> If not, I'd turn this page into a table of links to the equivalent
>> pages for the other projects.
>
> Agreed.
>
>> My own feeling is that when it comes to documentation, less is more
>> (or it should be as modular as possible). I hate it when GBrowse
>> starts telling me precisely how to install Apache and MySQL, but
>> apparently some people like it like that.
>
> GBrowse users are fairly diverse (ranging from users well-versed with SQL/Apache/etc and other not so much:). ?I would rather have too much documentation, but have it be well-organized to the point where more experienced users can bypass certain instructions.

Agreed.

I think the MediaWiki documentation on www.mediawiki.org is a good
example. With tutorials, TOCs, pages for specific settings and good
use of categories. In my (limited) experience, only the bioperl wiki
comes close to this standard.

Anyway, I'm probably trolling way off topic with that last remark.


> chris
>
>> On 5 March 2011 22:11, Jason Stajich <jason.stajich at gmail.com> wrote:
>>> This is probably also a message that would be helpful to generally get
>>> members from the various projects involved.
>>>
>>> -------- Original Message --------
>>> From: ? Hilmar Lapp <hlapp at drycafe.net>
>>> Subject: ? ? ? ?[Root-l] Source Code page on OBF wiki
>>> Date: ? Sat, 5 Mar 2011 13:59:49 -0500
>>> To: ? ? Root-l <root-l at open-bio.org>
>>>
>>>
>>>
>>> This page seems highly outdated: http://open-bio.org/wiki/SourceCode
>>>
>>> I could take a stab at correcting some of the stuff, but don't even
>>> have the complete picture necessary to fix it, so if someone who does
>>> would do so that'd be great help. I'm also wondering to what extent we
>>> should trim down the information here and link to the individual
>>> project wikis instead.
>>>
>>> I got here from the BioSQL wiki which links there for instructions on
>>> obtaining source code through anonymous svn access. That doesn't apply
>>> anymore, but there also is no section on anonymously obtaining code
>>> through git. One question I'm asking myself is whether we even need to
>>> document that, given that Github explains it already.
>>>
>>> Anyone any thoughts on what we should focus on in this page?
>>>
>>> ? ? ? ?-hilmar
>>> --
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Root-l mailing list
>>> Root-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/root-l
>>>
>>> _______________________________________________
>>> Open-Bio-l mailing list
>>> Open-Bio-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>>
>>
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>
>


From dag at sonsorol.org  Mon Mar  7 08:54:39 2011
From: dag at sonsorol.org (Chris Dagdigian)
Date: Mon, 07 Mar 2011 08:54:39 -0500
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTim_V6K0zBXc7kMSBei_cTDuW_mj9YrM4XsvBjp4@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>	<AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>	<AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
	<AANLkTim_V6K0zBXc7kMSBei_cTDuW_mj9YrM4XsvBjp4@mail.gmail.com>
Message-ID: <4D74E39F.1040601@sonsorol.org>


Our cloud servers are running on tiny T1.micro slice EC2 server 
instances which have between 1-2 CPUs at any given time and about 768MB 
of RAM.

For OBF these are the most reasonable priced systems, I don't even want 
to step up to the m1.small servers because at .8 to .10 cents an hour 
the costs gets somewhat pricy compared to what I can scrounge for VMs 
and "donate" to OBF. That said though if OBF wanted to purchase a 
reserved instance or two we could get the price down significantly.

testing.open-bio.org may not have enough power to run the Tomcat stack + 
Maven.

That said though, I have access to VMs and resources outside of the 
cloud and it's trivial to add new ones, especially for systems that do 
not need a front-facing internet IP address.

I also like the HTTP redirect option, that seems reasonable to do as well.

Anyway OBF can always fire up more cloud instances but since that costs 
money the request needs go through the OBF Board.
-dag





Peter Cock wrote:
> On Fri, Mar 4, 2011 at 5:14 PM, Andreas Prlic<andreas at sdsc.edu>  wrote:
>>> You mean it runs the unit tests itself? Hmm - that may not fit with
>>> type of Amazon machine Chris D is renting for testing.open-bio.org
>>> (buildbot doesn't do any heavy lifting - a separate pool of slaves
>>> run the unit tests).
>> Yes, running junit tests is part of the Maven release process. (you
>> can only make a release if the code compiles and all tests are
>> passed). Since Java is coming with its own VM, we don't need to test
>> on all possible architectures. Considering this, perhaps it would be
>> sufficient to redirect http://testing.open-bio.org/biojava/ to
>> http://source.rcsb.org:8080/cruisecontrol/  ...
>
> That sounds like a practical short term solution :)
>
> Let's give Chris D a chance to comment though.
>
> Peter

From cjfields at illinois.edu  Wed Mar 16 13:58:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 12:58:23 -0500
Subject: [Open-bio-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
Message-ID: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>

(apologies if you receive multiple copies of this)

All,

We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:

http://redmine.open-bio.org/

All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.

For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:

1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.

2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.

Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.

Let us know if you have any questions.  

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801

From cjfields at illinois.edu  Fri Mar 18 12:03:54 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 11:03:54 -0500
Subject: [Open-bio-l] Fwd: OpenID enabled on most wikis
References: <7ACFE455-FC0B-46BC-8C5D-66317E2D9CCA@illinois.edu>
Message-ID: <1D6757C7-9A2D-4A73-89EA-72147D48A5FA@illinois.edu>

(Thinking about it, this probably should have gone to open-bio-l, so here it is)

Begin forwarded message:

> From: Chris Fields <cjfields at illinois.edu>
> Date: March 18, 2011 11:02:55 AM CDT
> To: Bioroot <root-l at open-bio.org>
> Subject: OpenID enabled on most wikis
> 
> Just to post that OpenID is now enabled on most wikis and is the only way new users can login to edit (the BioLib wiki is a notable exception, Pjotr wanted to manually approve new user accounts).  The old login link is still present but new account creation is not allowed except by sysadmins.
> 
> I already posted this to the news blogs, but I suppose we need to add something else to the wikis indicating this for new users?  
> 
> chris



From rmb32 at cornell.edu  Fri Mar 18 15:26:14 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 18 Mar 2011 15:26:14 -0400
Subject: [Open-bio-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4D83B1D6.3080703@cornell.edu>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2011 FAQ at http://bit.ly/hpoz8W

Student applications are due April 8, 2011 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2011 Administrator



From dan.bolser at gmail.com  Sat Mar 19 07:21:17 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sat, 19 Mar 2011 11:21:17 +0000
Subject: [Open-bio-l] Fwd: OpenID enabled on most wikis
In-Reply-To: <1D6757C7-9A2D-4A73-89EA-72147D48A5FA@illinois.edu>
References: <7ACFE455-FC0B-46BC-8C5D-66317E2D9CCA@illinois.edu>
	<1D6757C7-9A2D-4A73-89EA-72147D48A5FA@illinois.edu>
Message-ID: <AANLkTi=ZkMiUv9RcM4q1gyhR+8wx8-OjyL8r7XrV0v9A@mail.gmail.com>

On 18 March 2011 16:03, Chris Fields <cjfields at illinois.edu> wrote:
> (Thinking about it, this probably should have gone to open-bio-l, so here it is)
>
> Begin forwarded message:
>
>> From: Chris Fields <cjfields at illinois.edu>
>> Date: March 18, 2011 11:02:55 AM CDT
>> To: Bioroot <root-l at open-bio.org>
>> Subject: OpenID enabled on most wikis
>>
>> Just to post that OpenID is now enabled on most wikis and is the only way new users can login to edit (the BioLib wiki is a notable exception, Pjotr wanted to manually approve new user accounts). ?The old login link is still present but new account creation is not allowed except by sysadmins.
>>
>> I already posted this to the news blogs, but I suppose we need to add something else to the wikis indicating this for new users?

Edit one of the system messages that appear on the login pages?

Is there a formal procedure for getting a particular extension or
other added to the obf wiki farm?


Cheers,
Dan.

>> chris
>
>
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>


From maisiliuma at gmail.com  Sun Mar  6 23:12:40 2011
From: maisiliuma at gmail.com (mais ar)
Date: Mon, 07 Mar 2011 04:12:40 -0000
Subject: [Open-bio-l] Bioinformatics
Message-ID: <AANLkTimMDPxGpxniXGnXxGH93L5T_EGhx6w3RfcVZe9c@mail.gmail.com>

Dear all,

      I'm having the promoter sequence. I want to know the domains,
transcriptors etc.. from the promoter Sequence.......... Any ideas,
suggestion pls......... Is there any softwares available.? Pls send me soon,
Thanks in advance.

Regards,
Uma.

From cjfields at illinois.edu  Tue Mar 29 16:33:27 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 29 Mar 2011 15:33:27 -0500
Subject: [Open-bio-l] Redmine and SSL
Message-ID: <3BDCA019-CCFD-4F47-8C90-57FD4E1684CF@illinois.edu>

All,

Just an update: since SSL authentication was added for redmine and everything has switched from http->https, in order for post-receive hooks from GitHub to work you will likely need to update the URL from http to https.  Just found this out myself testing bioperl commits with ref IDs in the commit messages.

chris

From rmb32 at cornell.edu  Tue Mar 29 17:20:41 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 29 Mar 2011 14:20:41 -0700
Subject: [Open-bio-l] Announcing OBF Summer of Code - please forward!
Message-ID: <4D924D29.3020707@cornell.edu>

Hi all,

Here's an advertising-ready announcement for OBF's Summer of Code, 
thanks to Christian Zmasek and Hilmar Lapp for their excellent writing.

Student applications are due April 8!  Please spread it widely, we need 
to reach lots of students with it!

Rob Buels
OBF GSoC 2011 Admin


============================================================

*** Please disseminate widely at your local institutions ***
*** including posting to message and job boards, so that ***
*** we reach as many students as possible.               ***

============================================================


OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011

Applications due 19:00 UTC, April 8, 2010.
http://www.open-bio.org/wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation Summer of Code program provides a 
unique opportunity for undergraduate, masters, and PhD students to 
obtain hands-on experience writing and extending open-source software 
for bioinformatics under the mentorship of experienced developers from 
around the world. The program is the participation of the Open 
Bioinformatics Foundation (OBF) as a mentoring organization in the 
Google Summer of Code(tm) (http://code.google.com/soc/).

Students successfully completing the 3 month program receive a $5,000 
USD stipend, and may work entirely from their home or home institution. 
  Participation is open to students from any country in the world except 
countries subject to US trade restrictions.  Each student will have at 
least one dedicated mentor to show them the ropes and help them complete 
their project.

The Open Bioinformatics Foundation is particularly seeking students 
interested in both bioinformatics (computational biology) and software 
development. Some initial project ideas are listed on the website. These 
range from Galaxy phylogenetics pipeline development in Biopython to 
lightweight sequence objects and lazy parsing in BioPerl, a DAS Server 
for large files on local filesystems, and mapping Java libraries to 
Perl/Ruby/Python using Biolib+SWIG+JNI.  All project ideas are flexible 
and many can be adjusted in scope to match the skills of the student. We 
also welcome and encourage students proposing their own project ideas; 
historically some of the most successful Summer of Code projects are 
ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website 
(http://socghop.appspot.com/), where you will also find GSoC program 
rules and eligibility requirements. The 12-day application period for 
students runs from Monday, March 28 through Friday, April 8th, 2011.

INQUIRIES:

We strongly encourage all interested students to get in touch with us 
with their ideas as early on as possible.  See the OBF GSoC page for 
contact details.

2011 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs




From bonnalraoul at ingm.it  Tue Mar  1 10:03:18 2011
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Tue, 1 Mar 2011 11:03:18 +0100
Subject: [Open-bio-l] [NGS] Design, Normalization, DiffExpression
Message-ID: <9C59CA8E-8B0A-4DB8-B9E2-88E6113D241E@ingm.it>


http://www.silencejournal.com/content/2/1/2/abstract

--
Ra

linkedin: http://it.linkedin.com/in/raoulbonnal
twitter: http://twitter.com/ilpuccio
skype: ilpuccio
irc.freenode.net: Helius
github: https://github.com/helios








From biopython at maubp.freeserve.co.uk  Thu Mar  3 13:17:39 2011
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 3 Mar 2011 13:17:39 +0000
Subject: [Open-bio-l] Moving from Bugzilla to Redmine on a cloud server
Message-ID: <AANLkTi=NRYHCrzsn6uttQyGdPGNtrX4YDEqGRvQn0k=p@mail.gmail.com>

Hi all,

This is a continuation of discussions on root-l and also on biojava-dev about
the Bio* project's bug tracker, which currently uses Bugzilla running on an
OBF hosted machine - http://bugzilla.open-bio.org/

http://lists.open-bio.org/pipermail/biojava-dev/2011-March/004582.html

Chris and Jason have been looking at using Redmine running on the Amazon
cloud, in part to simplify OBF server maintainance, and how to migrate the
Bugzilla data over to this.

Note that the open-bio-l mailing list archive is public, so keep that in mind
regarding passwords etc. See:

http://lists.open-bio.org/pipermail/open-bio-l/

Peter

---------- Forwarded message ----------
From: Peter <biopython at maubp.freeserve.co.uk>
Date: Thu, Mar 3, 2011 at 1:11 PM
Subject: Re: [Biojava-dev] Open bugs.
To: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>
Cc: Jason Stajich <jason.stajich at gmail.com>, Chris Dagdigian <chris at bioteam.net>


On Wed, Mar 2, 2011 at 2:23 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
> Thanks, Peter. As far as I know none of us is on the root-l, however a while ago
> Scooter and I suggested to get redmine installed on a vm on the support list. I
> was already wondering about the status of this since we never heard back....
> Can you give us a status update of this discussion?

There was some discussion on root-l (usually used for sys-admin stuff) with
Andreas etc CC'd. The root-l list is private (with no public archive) as often
general sensitive server details (e.g. host names, port numbers, and access
credentials) are discussed. However, I think there was broad agreement
that most of the RedMine discussion could happen in the open, probably
on the Open-Bio-l list. Anyone interested sign up here:
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Meanwhile, Chris has been blogging about some of his experiences:
http://blog.bioteam.net/2011/02/amazon-cloudformation-first-look/
http://blog.bioteam.net/2011/03/amazon-cloudformation-second-look/

Peter


From p.j.a.cock at googlemail.com  Fri Mar  4 11:45:11 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 11:45:11 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
Message-ID: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>

Hi all,

I've retitled this thread to reflect the current topic, and CC'd the open-bio-l
mailing list as Raoul suggested. Can we continue the discussion there?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>
>> Dear All,
>> a) this discussion is a good starting point for a workgroup during Codefest
>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>> testing our projects ?! It would be fun to see all the bio* with stats about
>> testing etc...
>
> I think the buildbot instance covers some of that, but they are mainly
> automated builds:
>
> http://testing.open-bio.org/
>
> biopython is the only one set up currently.

Note that this is a small Amazon cloud machine, and doesn't actually run
the tests itself (that would require a more expensive machine due to the
higher load). Instead we need client machines (covering a range of OS,
Python version etc) whose run-time is donated (currently by Biopython
developers or their employers).

When setting up http://testing.open-bio.org/ the intention was to have
it host other Bio* projects too - and they don't have to be using the
buildbot software (but they could if they wanted to).

>> b) testing is very important and new contributes should be accepted
>> only with tests, which implies a problem how to check fake tests? :-)
>
> Code review and checking the test results. ?Otherwise, you have to trust
> your developers.

This is something we're pushing much more with Biopython in recent
years (a depressing amount of legacy code had no tests when I first
got involved, things are a lot better now). For any new code contributions
we do ask for tests and minimal documentation (and try and work
with the contributor to help this happen).

>> c) usually ruby's community relies a lot on doc==tests that's
>> completely wrong, because the newbies can't read fluently the
>> code, also because there are different tools and sometimes a lot
>> of mocking.

With Biopython we're starting to make more use of testable docs
(Python's doctest system) which is really good I think. But you are
right, you need proper unit tests AS WELL. With our doctests,
the primary aim is to be useful documentation (which can double
as a basic functional test).

>> c.a) recently i had an idea, but I have no time to do that: establish
>> a relationship between a mock and a real object and validate the
>> mock or enable it only if the real object has been tested before.
>> That would make mocking more sens to me, but i think this is
>> another story.
>
> Yes, I've thought about that as well re: Moose-based work, haven't
> wrapped my head around it either.

I'm not quite following - it may be a terminology difference.

>> d) I agree with Toshiaki, after this very useful brain storming
>> start working (Impressed to see all this traffic :-) )
>>
>> Cheers.
>
> +1. ?Will be interesting to see how things progress.
>
> chris

Same here :)

Peter



From p.j.a.cock at googlemail.com  Fri Mar  4 12:23:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 12:23:53 +0000
Subject: [Open-bio-l] Automated testing server for BioJava?
Message-ID: <AANLkTi=+6Z9hHNpwsNeK48V63yQO7yf9MMim5ds3+q8u@mail.gmail.com>

Hi all,

Just FYI, the OBF have a new (Amazon cloud) server running at
http://testing.open-bio.org which we are currently using to host
a buildbot for Biopython. Currently Tiago and I (from Biopython)
have been tinkering with this with help from Chris Dagdigian
on the sys-admin/cloud side.

The idea is that similar services could be setup for the other
Bio* projects (using buildbot or some other software), if you
are interested.

Note that this is a low power server and it is not intended to
be used to run tests itself - that is a job for separate build
slave machines (which should cover a range of OS,
python/java/perl/ruby versions etc).

For further discussion, can I point you here:
http://lists.open-bio.org/pipermail/open-bio-l/2011-March/000743.html

See also this BioRuby thread:
http://lists.open-bio.org/pipermail/bioruby/2011-March/001720.html
http://lists.open-bio.org/pipermail/bioruby/2011-March/001734.html

Regards,

Peter


From chapmanb at 50mail.com  Fri Mar  4 12:36:44 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 4 Mar 2011 07:36:44 -0500
Subject: [Open-bio-l] Bioinformatics Open Source Conference (BOSC
 2011)--Call for Abstracts
Message-ID: <20110304123644.GB27839@sobchak>

We invite you to submit an abstract to BOSC 2011! Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration". We
are also working to arrange a joint session with one of the other ISMB
SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student Travel
Awards for BOSC 2011. Each winner will be awarded $250 to defray the
costs of travel to BOSC 2011.
 
For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor 


From cjfields at illinois.edu  Fri Mar  4 14:14:12 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 08:14:12 -0600
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
Message-ID: <06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>

On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:

> Hi all,
> 
> I've retitled this thread to reflect the current topic, and CC'd the open-bio-l
> mailing list as Raoul suggested. Can we continue the discussion there?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l

Agreed.  I'm replying only on open-bio-l to promote that.

> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>> 
>>> Dear All,
>>> a) this discussion is a good starting point for a workgroup during Codefest
>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>> testing etc...
>> 
>> I think the buildbot instance covers some of that, but they are mainly
>> automated builds:
>> 
>> http://testing.open-bio.org/
>> 
>> biopython is the only one set up currently.
> 
> Note that this is a small Amazon cloud machine, and doesn't actually run
> the tests itself (that would require a more expensive machine due to the
> higher load). Instead we need client machines (covering a range of OS,
> Python version etc) whose run-time is donated (currently by Biopython
> developers or their employers).
> 
> When setting up http://testing.open-bio.org/ the intention was to have
> it host other Bio* projects too - and they don't have to be using the
> buildbot software (but they could if they wanted to).

I think it would be nice to have a smoke server there as well (I don't think buildbot can do that, AFAIK).  Will ask Chris D about it.

I like the fact that we now are diversifying beyond perl-based solutions with buildbot and redmine (I would include mediawiki, but PHP gives me the hives :).  Any easily-installable Java-based ones?

>>> b) testing is very important and new contributes should be accepted
>>> only with tests, which implies a problem how to check fake tests? :-)
>> 
>> Code review and checking the test results.  Otherwise, you have to trust
>> your developers.
> 
> This is something we're pushing much more with Biopython in recent
> years (a depressing amount of legacy code had no tests when I first
> got involved, things are a lot better now). For any new code contributions
> we do ask for tests and minimal documentation (and try and work
> with the contributor to help this happen).

Same here.  This is a common cycle with OS projects.

>>> c) usually ruby's community relies a lot on doc==tests that's
>>> completely wrong, because the newbies can't read fluently the
>>> code, also because there are different tools and sometimes a lot
>>> of mocking.
> 
> With Biopython we're starting to make more use of testable docs
> (Python's doctest system) which is really good I think. But you are
> right, you need proper unit tests AS WELL. With our doctests,
> the primary aim is to be useful documentation (which can double
> as a basic functional test).

The problem with bioperl is that much of the testing framework for in-line or testable docs wasn't present during the initial development process.  We also have a LOT of cruft modules that lack true author support. 

What we are planning on for future releases is to modularize bioperl installations, with an installer to put together the dists one wants.  The current release has well over 1000 classes and modules; modularizing will help remove some of the maintenance headaches we had been facing during development.  We are also pushing new code to go into separate CPAN installations, as these can be added to an installer as needed (as someone else long ago put it, we're essentially creating a mini-BioPerlPAN within CPAN).

>>> c.a) recently i had an idea, but I have no time to do that: establish
>>> a relationship between a mock and a real object and validate the
>>> mock or enable it only if the real object has been tested before.
>>> That would make mocking more sens to me, but i think this is
>>> another story.
>> 
>> Yes, I've thought about that as well re: Moose-based work, haven't
>> wrapped my head around it either.
> 
> I'm not quite following - it may be a terminology difference.

Perl thing; Moose makes tests using mocked objects a bit easier.  I have a side project that re-implements bioperl classes using Moose, has had some pretty promising results.

chris

>>> d) I agree with Toshiaki, after this very useful brain storming
>>> start working (Impressed to see all this traffic :-) )
>>> 
>>> Cheers.
>> 
>> +1.  Will be interesting to see how things progress.
>> 
>> chris
> 
> Same here :)
> 
> Peter




From p.j.a.cock at googlemail.com  Fri Mar  4 15:04:36 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 15:04:36 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
Message-ID: <AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>

On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>
>>>> Dear All,
>>>> a) this discussion is a good starting point for a workgroup during Codefest
>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>>> testing etc...
>>>
>>> I think the buildbot instance covers some of that, but they are mainly
>>> automated builds:
>>>
>>> http://testing.open-bio.org/
>>>
>>> biopython is the only one set up currently.
>>
>> Note that this is a small Amazon cloud machine, and doesn't actually run
>> the tests itself (that would require a more expensive machine due to the
>> higher load). Instead we need client machines (covering a range of OS,
>> Python version etc) whose run-time is donated (currently by Biopython
>> developers or their employers).
>>
>> When setting up http://testing.open-bio.org/ the intention was to have
>> it host other Bio* projects too - and they don't have to be using the
>> buildbot software (but they could if they wanted to).
>
> I think it would be nice to have a smoke server there as well (I don't
> think buildbot can do that, AFAIK). ?Will ask Chris D about it.

Can you clarify what you mean by smoke server? I'd assumed it was
a product name but now it sounds like you mean some methodology.

We have buildbot setup to do a nightly test of the latest code on all
the slaves. Additionally, via the web interface an admin can force a
rebuild, and force a build of the current latest code.

In theory one can also hook up buildbot to run tests triggered by
commits - I understand this isn't available for git repositories yet
though (at least, that's my recollection from dicussion with Tiago,
BCC'd in case he isn't on open-bio-l yet).

> I like the fact that we now are diversifying beyond perl-based
> solutions with buildbot and redmine (I would include mediawiki,
> but PHP gives me the hives :). ?Any easily-installable Java-based
> ones?

As long as the OBF has enough people familiar with the tool
to support it, I don't care what language it is written in.

>>>> b) testing is very important and new contributes should be accepted
>>>> only with tests, which implies a problem how to check fake tests? :-)
>>>
>>> Code review and checking the test results. ?Otherwise, you have to trust
>>> your developers.
>>
>> This is something we're pushing much more with Biopython in recent
>> years (a depressing amount of legacy code had no tests when I first
>> got involved, things are a lot better now). For any new code contributions
>> we do ask for tests and minimal documentation (and try and work
>> with the contributor to help this happen).
>
> Same here. ?This is a common cycle with OS projects.
>
>>>> c) usually ruby's community relies a lot on doc==tests that's
>>>> completely wrong, because the newbies can't read fluently the
>>>> code, also because there are different tools and sometimes a lot
>>>> of mocking.
>>
>> With Biopython we're starting to make more use of testable docs
>> (Python's doctest system) which is really good I think. But you are
>> right, you need proper unit tests AS WELL. With our doctests,
>> the primary aim is to be useful documentation (which can double
>> as a basic functional test).
>
> The problem with bioperl is that much of the testing framework
> for in-line or testable docs wasn't present during the initial
> development process. ?We also have a LOT of cruft modules
> that lack true author support.

Also true for Biopython to some extent.

> What we are planning on for future releases is to modularize
> bioperl installations, with an installer to put together the dists
> one wants. ?The current release has well over 1000 classes
> and modules; modularizing will help remove some of the
> maintenance headaches we had been facing during
> development. ?We are also pushing new code to go into
> separate CPAN installations, as these can be added to an
> installer as needed (as someone else long ago put it, we're
> essentially creating a mini-BioPerlPAN within CPAN).

I'm happy enough with the current Biopython monolith install -
although we are slowly gaining extra runtime dependencies,
doing the install/build is pretty easy. As the Python packaging
infrastructure matures, we too may want to consider
modularising - but for now I feel that is premature.

There is also an issue here for testing - if you can have a
diverse set of build slaves, then hopefully some will have
and some will lack each soft dependency. This is useful to
check graceful failure when things are missing.

Peter



From cjfields at illinois.edu  Fri Mar  4 15:58:01 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 09:58:01 -0600
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
Message-ID: <095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>

On Mar 4, 2011, at 9:04 AM, Peter Cock wrote:

> On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>> 
>>>>> Dear All,
>>>>> a) this discussion is a good starting point for a workgroup during Codefest
>>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>>>> testing etc...
>>>> 
>>>> I think the buildbot instance covers some of that, but they are mainly
>>>> automated builds:
>>>> 
>>>> http://testing.open-bio.org/
>>>> 
>>>> biopython is the only one set up currently.
>>> 
>>> Note that this is a small Amazon cloud machine, and doesn't actually run
>>> the tests itself (that would require a more expensive machine due to the
>>> higher load). Instead we need client machines (covering a range of OS,
>>> Python version etc) whose run-time is donated (currently by Biopython
>>> developers or their employers).
>>> 
>>> When setting up http://testing.open-bio.org/ the intention was to have
>>> it host other Bio* projects too - and they don't have to be using the
>>> buildbot software (but they could if they wanted to).
>> 
>> I think it would be nice to have a smoke server there as well (I don't
>> think buildbot can do that, AFAIK).  Will ask Chris D about it.
> 
> Can you clarify what you mean by smoke server? I'd assumed it was
> a product name but now it sounds like you mean some methodology.
> 
> We have buildbot setup to do a nightly test of the latest code on all
> the slaves. Additionally, via the web interface an admin can force a
> rebuild, and force a build of the current latest code.
> 
> In theory one can also hook up buildbot to run tests triggered by
> commits - I understand this isn't available for git repositories yet
> though (at least, that's my recollection from dicussion with Tiago,
> BCC'd in case he isn't on open-bio-l yet).

A smoke server holds test results submitted from users, or really anyone who has a set of modules/tools installed; it can be part of the build/testing process.  It's less automated building and more distributed than buildbot: the server doesn't call out to a specific set of build servers to run builds and tests, but relies on the community (developers, users) to run tests and submit them.  CPAN has this built in via CPAN Testers; one can install a set of modules and then, every time a dist is installed via CPAN a test report is sent to a remote server:

http://www.cpantesters.org/distro/B/bioperl.html

This is similar to what the bioruby folks are searching for, if I'm not mistaken.  

(Just so there is no confusion, in most cases with software 'smoke testing' refers to a set of prelim tests to make sure a build works, but in practice with small projects the term equally applies to running every test)

>> I like the fact that we now are diversifying beyond perl-based
>> solutions with buildbot and redmine (I would include mediawiki,
>> but PHP gives me the hives :).  Any easily-installable Java-based
>> ones?
> 
> As long as the OBF has enough people familiar with the tool
> to support it, I don't care what language it is written in.

Same here.

chris





From andreas at sdsc.edu  Fri Mar  4 16:34:39 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Mar 2011 08:34:39 -0800
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
Message-ID: <AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>

Just to quickly add, for BioJava, we are already using CruiseControl
for automated testing, building and making nightly releases. I am
hosting this on one of my work servers:
http://source.rcsb.org:8080/cruisecontrol/  but would be happy if this
would be moved to an OBF service.

Only issue with this system is that mailman keeps filtering out the
notification emails that are being generated if one of the junit tests
(or compilation) fails, so I still have to myself keep chasing
developers who break the build.

Andreas

On Fri, Mar 4, 2011 at 7:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 4, 2011, at 9:04 AM, Peter Cock wrote:
>
>> On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>>>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>>>
>>>>>> Dear All,
>>>>>> a) this discussion is a good starting point for a workgroup during Codefest
>>>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr
>>>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>>>> testing our projects ?! It would be fun to see all the bio* with stats about
>>>>>> testing etc...
>>>>>
>>>>> I think the buildbot instance covers some of that, but they are mainly
>>>>> automated builds:
>>>>>
>>>>> http://testing.open-bio.org/
>>>>>
>>>>> biopython is the only one set up currently.
>>>>
>>>> Note that this is a small Amazon cloud machine, and doesn't actually run
>>>> the tests itself (that would require a more expensive machine due to the
>>>> higher load). Instead we need client machines (covering a range of OS,
>>>> Python version etc) whose run-time is donated (currently by Biopython
>>>> developers or their employers).
>>>>
>>>> When setting up http://testing.open-bio.org/ the intention was to have
>>>> it host other Bio* projects too - and they don't have to be using the
>>>> buildbot software (but they could if they wanted to).
>>>
>>> I think it would be nice to have a smoke server there as well (I don't
>>> think buildbot can do that, AFAIK). ?Will ask Chris D about it.
>>
>> Can you clarify what you mean by smoke server? I'd assumed it was
>> a product name but now it sounds like you mean some methodology.
>>
>> We have buildbot setup to do a nightly test of the latest code on all
>> the slaves. Additionally, via the web interface an admin can force a
>> rebuild, and force a build of the current latest code.
>>
>> In theory one can also hook up buildbot to run tests triggered by
>> commits - I understand this isn't available for git repositories yet
>> though (at least, that's my recollection from dicussion with Tiago,
>> BCC'd in case he isn't on open-bio-l yet).
>
> A smoke server holds test results submitted from users, or really anyone who has a set of modules/tools installed; it can be part of the build/testing process. ?It's less automated building and more distributed than buildbot: the server doesn't call out to a specific set of build servers to run builds and tests, but relies on the community (developers, users) to run tests and submit them. ?CPAN has this built in via CPAN Testers; one can install a set of modules and then, every time a dist is installed via CPAN a test report is sent to a remote server:
>
> http://www.cpantesters.org/distro/B/bioperl.html
>
> This is similar to what the bioruby folks are searching for, if I'm not mistaken.
>
> (Just so there is no confusion, in most cases with software 'smoke testing' refers to a set of prelim tests to make sure a build works, but in practice with small projects the term equally applies to running every test)
>
>>> I like the fact that we now are diversifying beyond perl-based
>>> solutions with buildbot and redmine (I would include mediawiki,
>>> but PHP gives me the hives :). ?Any easily-installable Java-based
>>> ones?
>>
>> As long as the OBF has enough people familiar with the tool
>> to support it, I don't care what language it is written in.
>
> Same here.
>
> chris
>
>
>
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------



From p.j.a.cock at googlemail.com  Fri Mar  4 16:45:32 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 16:45:32 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
Message-ID: <AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>

On Fri, Mar 4, 2011 at 4:34 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Just to quickly add, for BioJava, we are already using CruiseControl
> for automated testing, building and making nightly releases. I am
> hosting this on one of my work servers:
> http://source.rcsb.org:8080/cruisecontrol/ ?but would be happy if this
> would be moved to an OBF service.

I see, from http://cruisecontrol.sourceforge.net/

Would you be happy with http://testing.open-bio.org/biojava/ as the URL?

Are there any gotchas with installing it? e.g. dependencies? I guess
you'll need to contact Chris D to get access to the machine and
also sign up to root-l to keep you in the loop with any sys admin.
He'll probably want to know things like expected machine load
(e.g. is it RAM hungry?).

> Only issue with this system is that mailman keeps filtering out the
> notification emails that are being generated if one of the junit tests
> (or compilation) fails, so I still have to myself keep chasing
> developers who break the build.

So far I'm getting buildbot emails from testing.open-bio.org so
you may find it works OK from the new location.

Peter



From andreas at sdsc.edu  Fri Mar  4 16:59:15 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Mar 2011 08:59:15 -0800
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
Message-ID: <AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>

> I see, from http://cruisecontrol.sourceforge.net/

correct

> Would you be happy with http://testing.open-bio.org/biojava/ as the URL?

sure

> Are there any gotchas with installing it?

it is all in Java and requires also a Tomcat server running on one
port. There was something about not having too much CPU available on
the VM? Some of the junit tests in biojava require a bit of CPU. RAM
requirement currently is < 512M and finally SSH keys have to be set up
so the build system can upload the latest biojava snapshots to the
Maven build archive...


> So far I'm getting buildbot emails from testing.open-bio.org so
> you may find it works OK from the new location.

problem is not the sending of the mails but getting them accepted on
biojava-l and -dev. They keep getting flagged as suspicious mails due
to the long HTML content.

Andreas

>
> Peter
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From p.j.a.cock at googlemail.com  Fri Mar  4 17:08:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 17:08:58 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
Message-ID: <AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>

On Fri, Mar 4, 2011 at 4:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> I see, from http://cruisecontrol.sourceforge.net/
>
> correct
>
>> Would you be happy with http://testing.open-bio.org/biojava/ as the URL?
>
> sure
>
>> Are there any gotchas with installing it?
>
> it is all in Java and requires also a Tomcat server running on one
> port. There was something about not having too much CPU available on
> the VM? Some of the junit tests in biojava require a bit of CPU. RAM
> requirement currently is < 512M and finally SSH keys have to be set up
> so the build system can upload the latest biojava snapshots to the
> Maven build archive...

You mean it runs the unit tests itself? Hmm - that may not fit with
type of Amazon machine Chris D is renting for testing.open-bio.org
(buildbot doesn't do any heavy lifting - a separate pool of slaves
run the unit tests).

>> So far I'm getting buildbot emails from testing.open-bio.org so
>> you may find it works OK from the new location.
>
> problem is not the sending of the mails but getting them accepted on
> biojava-l and -dev. They keep getting flagged as suspicious mails due
> to the long HTML content.

OK - I assumed it would be down to the sender's DNS or something.
As you say, long HTML content is a different issue.

Peter


From andreas at sdsc.edu  Fri Mar  4 17:14:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Mar 2011 09:14:57 -0800
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
	<AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>
Message-ID: <AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>

> You mean it runs the unit tests itself? Hmm - that may not fit with
> type of Amazon machine Chris D is renting for testing.open-bio.org
> (buildbot doesn't do any heavy lifting - a separate pool of slaves
> run the unit tests).

Yes, running junit tests is part of the Maven release process. (you
can only make a release if the code compiles and all tests are
passed). Since Java is coming with its own VM, we don't need to test
on all possible architectures. Considering this, perhaps it would be
sufficient to redirect http://testing.open-bio.org/biojava/ to
http://source.rcsb.org:8080/cruisecontrol/  ...

Andreas


From p.j.a.cock at googlemail.com  Fri Mar  4 17:20:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Mar 2011 17:20:53 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>
	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>
	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>
	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>
	<AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>
	<AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
Message-ID: <AANLkTim_V6K0zBXc7kMSBei_cTDuW_mj9YrM4XsvBjp4@mail.gmail.com>

On Fri, Mar 4, 2011 at 5:14 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> You mean it runs the unit tests itself? Hmm - that may not fit with
>> type of Amazon machine Chris D is renting for testing.open-bio.org
>> (buildbot doesn't do any heavy lifting - a separate pool of slaves
>> run the unit tests).
>
> Yes, running junit tests is part of the Maven release process. (you
> can only make a release if the code compiles and all tests are
> passed). Since Java is coming with its own VM, we don't need to test
> on all possible architectures. Considering this, perhaps it would be
> sufficient to redirect http://testing.open-bio.org/biojava/ to
> http://source.rcsb.org:8080/cruisecontrol/ ?...

That sounds like a practical short term solution :)

Let's give Chris D a chance to comment though.

Peter



From heuermh at acm.org  Fri Mar  4 21:09:13 2011
From: heuermh at acm.org (Michael Heuer)
Date: Fri, 4 Mar 2011 16:09:13 -0500 (EST)
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.1103041557020.16914-100000@shell3.shore.net>

On Fri, 4 Mar 2011, Andreas Prlic wrote:

> > You mean it runs the unit tests itself? Hmm - that may not fit with
> > type of Amazon machine Chris D is renting for testing.open-bio.org
> > (buildbot doesn't do any heavy lifting - a separate pool of slaves
> > run the unit tests).
>
> Yes, running junit tests is part of the Maven release process. (you
> can only make a release if the code compiles and all tests are
> passed). Since Java is coming with its own VM, we don't need to test
> on all possible architectures. Considering this, perhaps it would be
> sufficient to redirect http://testing.open-bio.org/biojava/ to
> http://source.rcsb.org:8080/cruisecontrol/  ...

Hello Andreas,

Hudson/Jenkins/Nectar/whatever you want to call it has support for build
slave instances, with Amazon EC2 cloud support and such.  Perhaps it might
be possible to set it up on testing.open-bio.org and farm out to rcsb.org
and/or other sites.

http://cloudbees.com
http://nectar.cloudbees.com
http://jenkins-ci.org
http://hudson-ci.org

   michael



From tiagoantao at gmail.com  Fri Mar  4 15:36:57 2011
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Fri, 4 Mar 2011 15:36:57 +0000
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>
	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>
	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>
Message-ID: <AANLkTikJBhXANjgyESy8NSj5Zhj3V5X-iKpNrC_ozok0@mail.gmail.com>

On mobile phone, fast mail. Buidbot CAN be trigerred by git commits.

2011/3/4, Peter Cock <p.j.a.cock at googlemail.com>:
> On Fri, Mar 4, 2011 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> On Mar 4, 2011, at 5:45 AM, Peter Cock wrote:
>>> On Thu, Mar 3, 2011 at 8:52 PM, Chris Fields <cjfields at illinois.edu>
>>> wrote:
>>>> On Mar 3, 2011, at 2:29 PM, Raoul Bonnal wrote:
>>>>
>>>>> Dear All,
>>>>> a) this discussion is a good starting point for a workgroup during
>>>>> Codefest
>>>>> 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the
>>>>> addr
>>>>> here, sorry) a.idea) why not create a common "machine" on the cloud for
>>>>> testing our projects ?! It would be fun to see all the bio* with stats
>>>>> about
>>>>> testing etc...
>>>>
>>>> I think the buildbot instance covers some of that, but they are mainly
>>>> automated builds:
>>>>
>>>> http://testing.open-bio.org/
>>>>
>>>> biopython is the only one set up currently.
>>>
>>> Note that this is a small Amazon cloud machine, and doesn't actually run
>>> the tests itself (that would require a more expensive machine due to the
>>> higher load). Instead we need client machines (covering a range of OS,
>>> Python version etc) whose run-time is donated (currently by Biopython
>>> developers or their employers).
>>>
>>> When setting up http://testing.open-bio.org/ the intention was to have
>>> it host other Bio* projects too - and they don't have to be using the
>>> buildbot software (but they could if they wanted to).
>>
>> I think it would be nice to have a smoke server there as well (I don't
>> think buildbot can do that, AFAIK). ?Will ask Chris D about it.
>
> Can you clarify what you mean by smoke server? I'd assumed it was
> a product name but now it sounds like you mean some methodology.
>
> We have buildbot setup to do a nightly test of the latest code on all
> the slaves. Additionally, via the web interface an admin can force a
> rebuild, and force a build of the current latest code.
>
> In theory one can also hook up buildbot to run tests triggered by
> commits - I understand this isn't available for git repositories yet
> though (at least, that's my recollection from dicussion with Tiago,
> BCC'd in case he isn't on open-bio-l yet).
>
>> I like the fact that we now are diversifying beyond perl-based
>> solutions with buildbot and redmine (I would include mediawiki,
>> but PHP gives me the hives :). ?Any easily-installable Java-based
>> ones?
>
> As long as the OBF has enough people familiar with the tool
> to support it, I don't care what language it is written in.
>
>>>>> b) testing is very important and new contributes should be accepted
>>>>> only with tests, which implies a problem how to check fake tests? :-)
>>>>
>>>> Code review and checking the test results. ?Otherwise, you have to trust
>>>> your developers.
>>>
>>> This is something we're pushing much more with Biopython in recent
>>> years (a depressing amount of legacy code had no tests when I first
>>> got involved, things are a lot better now). For any new code
>>> contributions
>>> we do ask for tests and minimal documentation (and try and work
>>> with the contributor to help this happen).
>>
>> Same here. ?This is a common cycle with OS projects.
>>
>>>>> c) usually ruby's community relies a lot on doc==tests that's
>>>>> completely wrong, because the newbies can't read fluently the
>>>>> code, also because there are different tools and sometimes a lot
>>>>> of mocking.
>>>
>>> With Biopython we're starting to make more use of testable docs
>>> (Python's doctest system) which is really good I think. But you are
>>> right, you need proper unit tests AS WELL. With our doctests,
>>> the primary aim is to be useful documentation (which can double
>>> as a basic functional test).
>>
>> The problem with bioperl is that much of the testing framework
>> for in-line or testable docs wasn't present during the initial
>> development process. ?We also have a LOT of cruft modules
>> that lack true author support.
>
> Also true for Biopython to some extent.
>
>> What we are planning on for future releases is to modularize
>> bioperl installations, with an installer to put together the dists
>> one wants. ?The current release has well over 1000 classes
>> and modules; modularizing will help remove some of the
>> maintenance headaches we had been facing during
>> development. ?We are also pushing new code to go into
>> separate CPAN installations, as these can be added to an
>> installer as needed (as someone else long ago put it, we're
>> essentially creating a mini-BioPerlPAN within CPAN).
>
> I'm happy enough with the current Biopython monolith install -
> although we are slowly gaining extra runtime dependencies,
> doing the install/build is pretty easy. As the Python packaging
> infrastructure matures, we too may want to consider
> modularising - but for now I feel that is premature.
>
> There is also an issue here for testing - if you can have a
> diverse set of build slaves, then hopefully some will have
> and some will lack each soft dependency. This is useful to
> check graceful failure when things are missing.
>
> Peter
>

-- 
Enviada a partir do meu dispositivo m?vel

"If you want to get laid, go to college.  If you want an education, go
to the library." - Frank Zappa



From jason.stajich at gmail.com  Sat Mar  5 22:11:19 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 05 Mar 2011 14:11:19 -0800
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
Message-ID: <4D72B507.802@gmail.com>

This is probably also a message that would be helpful to generally get 
members from the various projects involved.

-------- Original Message --------
From: 	Hilmar Lapp <hlapp at drycafe.net>
Subject: 	[Root-l] Source Code page on OBF wiki
Date: 	Sat, 5 Mar 2011 13:59:49 -0500
To: 	Root-l <root-l at open-bio.org>



This page seems highly outdated: http://open-bio.org/wiki/SourceCode

I could take a stab at correcting some of the stuff, but don't even
have the complete picture necessary to fix it, so if someone who does
would do so that'd be great help. I'm also wondering to what extent we
should trim down the information here and link to the individual
project wikis instead.

I got here from the BioSQL wiki which links there for instructions on
obtaining source code through anonymous svn access. That doesn't apply
anymore, but there also is no section on anonymously obtaining code
through git. One question I'm asking myself is whether we even need to
document that, given that Github explains it already.

Anyone any thoughts on what we should focus on in this page?

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================




_______________________________________________
Root-l mailing list
Root-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/root-l



From jason.stajich at gmail.com  Sat Mar  5 22:25:10 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 05 Mar 2011 14:25:10 -0800
Subject: [Open-bio-l] held msgs
Message-ID: <4D72B846.5000605@gmail.com>

Sorry - there were some held messages from last summer that were never 
moderated. I've allowed them through but that will explain the blast 
from the past.

-- 
Jason Stajich




From hlapp at drycafe.net  Sun Mar  6 02:58:04 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Mar 2011 21:58:04 -0500
Subject: [Open-bio-l] Job opening for GMOD User Support Specialist
Message-ID: <814155D1-1CD5-4E66-B726-2CF7E33EF3CE@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities. If you know someone who might be  
interested please forward.)

============================
GMOD User Support Specialist
============================

Are you fascinated by genomics and bioinformatics? Are you passionate  
about collaborative open-source software? Do you enjoy teaching and  
working with scientists?  If so, then this position is for you.

The Generic Model Organism Database project (GMOD) is a collection of  
open source software tools for creating and managing biological, and  
particularly genomic, databases.  GMOD has a large, highly  
distributed, and dynamic community of software users and developers.   
The University of North Carolina at Chapel Hill has an opening for a  
GMOD user support specialist, to be based at the US National  
Evolutionary Synthesis Center (NESCent, www.nescent.org) in Durham,  
North Carolina, while serving the international community of GMOD users.

Job Description:

The GMOD user support specialist will maintain online documentation;  
respond to mailing list help requests; present tutorials; organize  
short courses, conference sessions and other community building  
activities; survey user needs, and recruit members of the community to  
assist with these functions.   The incumbent will collaborate closely  
with the GMOD Coordinator (Scott Cain, The Ontario Institute for  
Cancer Research) and other distributed personnel.  See http://gmod.org/wiki/GMOD_Help_Desk 
  for more background on the activities of the user support  
specialist.  The salary range is $68,906 to $82,687, depending on  
qualifications, and the incumbent will receive a comprehensive  
benefits package as an SPA employee within the UNC system.

Qualifications:

Required qualifications include: excellent written and verbal  
communication skills; team orientation with strong interpersonal  
skills. Preferred qualifications include: an MS or PhD in biology,  
computer science or related field; three or more years of experience  
with web programming and relational database management systems; three  
or more years of experience with genome database administration or  
curation, preferably in a GMOD environment; at least one year of  
experience with web content management, ideally using MediaWiki;  
freedom to travel 5-15 weeks/yr.

To Apply:

Please provide a cover letter and CV, including contact information  
for three references, to Hilmar Lapp, Assistant Director of  
Informatics, NESCent, at hlapp at nescent.org, and submit materials  
through http://bit.ly/h9l74r.  Inquiries may be addressed to H. Lapp  
by email or by phone at 919.668.5288.

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From dan.bolser at gmail.com  Sun Mar  6 20:57:32 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 6 Mar 2011 20:57:32 +0000
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <4D72B507.802@gmail.com>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
	<4D72B507.802@gmail.com>
Message-ID: <AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>

Does open bio really house all the code from all these bio projects? I
guess not...

If not, I'd turn this page into a table of links to the equivalent
pages for the other projects.

My own feeling is that when it comes to documentation, less is more
(or it should be as modular as possible). I hate it when GBrowse
starts telling me precisely how to install Apache and MySQL, but
apparently some people like it like that.


On 5 March 2011 22:11, Jason Stajich <jason.stajich at gmail.com> wrote:
> This is probably also a message that would be helpful to generally get
> members from the various projects involved.
>
> -------- Original Message --------
> From: ? Hilmar Lapp <hlapp at drycafe.net>
> Subject: ? ? ? ?[Root-l] Source Code page on OBF wiki
> Date: ? Sat, 5 Mar 2011 13:59:49 -0500
> To: ? ? Root-l <root-l at open-bio.org>
>
>
>
> This page seems highly outdated: http://open-bio.org/wiki/SourceCode
>
> I could take a stab at correcting some of the stuff, but don't even
> have the complete picture necessary to fix it, so if someone who does
> would do so that'd be great help. I'm also wondering to what extent we
> should trim down the information here and link to the individual
> project wikis instead.
>
> I got here from the BioSQL wiki which links there for instructions on
> obtaining source code through anonymous svn access. That doesn't apply
> anymore, but there also is no section on anonymously obtaining code
> through git. One question I'm asking myself is whether we even need to
> document that, given that Github explains it already.
>
> Anyone any thoughts on what we should focus on in this page?
>
> ? ? ? ?-hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
> _______________________________________________
> Root-l mailing list
> Root-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/root-l
>
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>



From cjfields at illinois.edu  Sun Mar  6 21:50:36 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 6 Mar 2011 15:50:36 -0600
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
	<4D72B507.802@gmail.com>
	<AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>
Message-ID: <14C9E6AB-8192-4941-972B-B5A601A37A74@illinois.edu>

On Mar 6, 2011, at 2:57 PM, Dan Bolser wrote:

> Does open bio really house all the code from all these bio projects? I
> guess not...

Depends on what you mean by 'house', all of these were present in open-bio version control (CVS/SVN) at one point, but most repos have recently migrated away from the open-bio-centric version control.  EMBOSS and a few others are still using CVS I think.

> If not, I'd turn this page into a table of links to the equivalent
> pages for the other projects.

Agreed.

> My own feeling is that when it comes to documentation, less is more
> (or it should be as modular as possible). I hate it when GBrowse
> starts telling me precisely how to install Apache and MySQL, but
> apparently some people like it like that.

GBrowse users are fairly diverse (ranging from users well-versed with SQL/Apache/etc and other not so much:).  I would rather have too much documentation, but have it be well-organized to the point where more experienced users can bypass certain instructions.

chris

> On 5 March 2011 22:11, Jason Stajich <jason.stajich at gmail.com> wrote:
>> This is probably also a message that would be helpful to generally get
>> members from the various projects involved.
>> 
>> -------- Original Message --------
>> From:   Hilmar Lapp <hlapp at drycafe.net>
>> Subject:        [Root-l] Source Code page on OBF wiki
>> Date:   Sat, 5 Mar 2011 13:59:49 -0500
>> To:     Root-l <root-l at open-bio.org>
>> 
>> 
>> 
>> This page seems highly outdated: http://open-bio.org/wiki/SourceCode
>> 
>> I could take a stab at correcting some of the stuff, but don't even
>> have the complete picture necessary to fix it, so if someone who does
>> would do so that'd be great help. I'm also wondering to what extent we
>> should trim down the information here and link to the individual
>> project wikis instead.
>> 
>> I got here from the BioSQL wiki which links there for instructions on
>> obtaining source code through anonymous svn access. That doesn't apply
>> anymore, but there also is no section on anonymously obtaining code
>> through git. One question I'm asking myself is whether we even need to
>> document that, given that Github explains it already.
>> 
>> Anyone any thoughts on what we should focus on in this page?
>> 
>>        -hilmar
>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Root-l mailing list
>> Root-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/root-l
>> 
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>> 
> 
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l




From dan.bolser at gmail.com  Mon Mar  7 09:21:19 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 7 Mar 2011 09:21:19 +0000
Subject: [Open-bio-l] Fwd: [Root-l] Source Code page on OBF wiki
In-Reply-To: <14C9E6AB-8192-4941-972B-B5A601A37A74@illinois.edu>
References: <FE8D10EC-8B56-43BD-A599-4B430F15425D@drycafe.net>
	<4D72B507.802@gmail.com>
	<AANLkTi=jGNNKrV109JRGVwi6ZZbYhzuHH_tgvGbnvbat@mail.gmail.com>
	<14C9E6AB-8192-4941-972B-B5A601A37A74@illinois.edu>
Message-ID: <AANLkTi=brtYKFV7E5Q+WnFVN6V_r2qUyqu4e2ZYqe9vw@mail.gmail.com>

On 6 March 2011 21:50, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 6, 2011, at 2:57 PM, Dan Bolser wrote:
>
>> Does open bio really house all the code from all these bio projects? I
>> guess not...
>
> Depends on what you mean by 'house', all of these were present in open-bio version control (CVS/SVN) at one point, but most repos have recently migrated away from the open-bio-centric version control. ?EMBOSS and a few others are still using CVS I think.
>
>> If not, I'd turn this page into a table of links to the equivalent
>> pages for the other projects.
>
> Agreed.
>
>> My own feeling is that when it comes to documentation, less is more
>> (or it should be as modular as possible). I hate it when GBrowse
>> starts telling me precisely how to install Apache and MySQL, but
>> apparently some people like it like that.
>
> GBrowse users are fairly diverse (ranging from users well-versed with SQL/Apache/etc and other not so much:). ?I would rather have too much documentation, but have it be well-organized to the point where more experienced users can bypass certain instructions.

Agreed.

I think the MediaWiki documentation on www.mediawiki.org is a good
example. With tutorials, TOCs, pages for specific settings and good
use of categories. In my (limited) experience, only the bioperl wiki
comes close to this standard.

Anyway, I'm probably trolling way off topic with that last remark.


> chris
>
>> On 5 March 2011 22:11, Jason Stajich <jason.stajich at gmail.com> wrote:
>>> This is probably also a message that would be helpful to generally get
>>> members from the various projects involved.
>>>
>>> -------- Original Message --------
>>> From: ? Hilmar Lapp <hlapp at drycafe.net>
>>> Subject: ? ? ? ?[Root-l] Source Code page on OBF wiki
>>> Date: ? Sat, 5 Mar 2011 13:59:49 -0500
>>> To: ? ? Root-l <root-l at open-bio.org>
>>>
>>>
>>>
>>> This page seems highly outdated: http://open-bio.org/wiki/SourceCode
>>>
>>> I could take a stab at correcting some of the stuff, but don't even
>>> have the complete picture necessary to fix it, so if someone who does
>>> would do so that'd be great help. I'm also wondering to what extent we
>>> should trim down the information here and link to the individual
>>> project wikis instead.
>>>
>>> I got here from the BioSQL wiki which links there for instructions on
>>> obtaining source code through anonymous svn access. That doesn't apply
>>> anymore, but there also is no section on anonymously obtaining code
>>> through git. One question I'm asking myself is whether we even need to
>>> document that, given that Github explains it already.
>>>
>>> Anyone any thoughts on what we should focus on in this page?
>>>
>>> ? ? ? ?-hilmar
>>> --
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Root-l mailing list
>>> Root-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/root-l
>>>
>>> _______________________________________________
>>> Open-Bio-l mailing list
>>> Open-Bio-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>>
>>
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>
>



From dag at sonsorol.org  Mon Mar  7 13:54:39 2011
From: dag at sonsorol.org (Chris Dagdigian)
Date: Mon, 07 Mar 2011 08:54:39 -0500
Subject: [Open-bio-l] Automated testing server; was [BioRuby] tutorial
In-Reply-To: <AANLkTim_V6K0zBXc7kMSBei_cTDuW_mj9YrM4XsvBjp4@mail.gmail.com>
References: <AANLkTik4LqbcQeV8qujtUTGNw0AeunRfYEtuSQR_tYHP@mail.gmail.com>	<06CDBAF4-CBAA-4230-8B7F-63380D53E292@illinois.edu>	<AANLkTinLx1dTSRTOeECT7QTjUnq7B12ZhL8BFoTSkijN@mail.gmail.com>	<095B1501-262A-44AC-B98B-D3A41999132D@illinois.edu>	<AANLkTi=EKNZibVZ4c0sMghi9n91HQ3Pk3iwbeUU28GA+@mail.gmail.com>	<AANLkTimDeZ8djSzc93eyWdE6HZOVOCoyq-h_7ZqLJ-m4@mail.gmail.com>	<AANLkTimLcfTD1Efv0e_1TpPJW0JsyBS==375qOFNgTmL@mail.gmail.com>	<AANLkTinwRwL9ueqMBUVxzt4-raXBe3vuZQzmHaf=GR0R@mail.gmail.com>	<AANLkTik9PtvyZmnjLqkgZ9rK2XAEJ2oPCvH9atQCh_=x@mail.gmail.com>
	<AANLkTim_V6K0zBXc7kMSBei_cTDuW_mj9YrM4XsvBjp4@mail.gmail.com>
Message-ID: <4D74E39F.1040601@sonsorol.org>


Our cloud servers are running on tiny T1.micro slice EC2 server 
instances which have between 1-2 CPUs at any given time and about 768MB 
of RAM.

For OBF these are the most reasonable priced systems, I don't even want 
to step up to the m1.small servers because at .8 to .10 cents an hour 
the costs gets somewhat pricy compared to what I can scrounge for VMs 
and "donate" to OBF. That said though if OBF wanted to purchase a 
reserved instance or two we could get the price down significantly.

testing.open-bio.org may not have enough power to run the Tomcat stack + 
Maven.

That said though, I have access to VMs and resources outside of the 
cloud and it's trivial to add new ones, especially for systems that do 
not need a front-facing internet IP address.

I also like the HTTP redirect option, that seems reasonable to do as well.

Anyway OBF can always fire up more cloud instances but since that costs 
money the request needs go through the OBF Board.
-dag





Peter Cock wrote:
> On Fri, Mar 4, 2011 at 5:14 PM, Andreas Prlic<andreas at sdsc.edu>  wrote:
>>> You mean it runs the unit tests itself? Hmm - that may not fit with
>>> type of Amazon machine Chris D is renting for testing.open-bio.org
>>> (buildbot doesn't do any heavy lifting - a separate pool of slaves
>>> run the unit tests).
>> Yes, running junit tests is part of the Maven release process. (you
>> can only make a release if the code compiles and all tests are
>> passed). Since Java is coming with its own VM, we don't need to test
>> on all possible architectures. Considering this, perhaps it would be
>> sufficient to redirect http://testing.open-bio.org/biojava/ to
>> http://source.rcsb.org:8080/cruisecontrol/  ...
>
> That sounds like a practical short term solution :)
>
> Let's give Chris D a chance to comment though.
>
> Peter


From cjfields at illinois.edu  Wed Mar 16 17:58:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 12:58:23 -0500
Subject: [Open-bio-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
Message-ID: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>

(apologies if you receive multiple copies of this)

All,

We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:

http://redmine.open-bio.org/

All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.

For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:

1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.

2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.

Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.

Let us know if you have any questions.  

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801


From cjfields at illinois.edu  Fri Mar 18 16:03:54 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 11:03:54 -0500
Subject: [Open-bio-l] Fwd: OpenID enabled on most wikis
References: <7ACFE455-FC0B-46BC-8C5D-66317E2D9CCA@illinois.edu>
Message-ID: <1D6757C7-9A2D-4A73-89EA-72147D48A5FA@illinois.edu>

(Thinking about it, this probably should have gone to open-bio-l, so here it is)

Begin forwarded message:

> From: Chris Fields <cjfields at illinois.edu>
> Date: March 18, 2011 11:02:55 AM CDT
> To: Bioroot <root-l at open-bio.org>
> Subject: OpenID enabled on most wikis
> 
> Just to post that OpenID is now enabled on most wikis and is the only way new users can login to edit (the BioLib wiki is a notable exception, Pjotr wanted to manually approve new user accounts).  The old login link is still present but new account creation is not allowed except by sysadmins.
> 
> I already posted this to the news blogs, but I suppose we need to add something else to the wikis indicating this for new users?  
> 
> chris




From rmb32 at cornell.edu  Fri Mar 18 19:26:14 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 18 Mar 2011 15:26:14 -0400
Subject: [Open-bio-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4D83B1D6.3080703@cornell.edu>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2011 FAQ at http://bit.ly/hpoz8W

Student applications are due April 8, 2011 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2011 Administrator




From dan.bolser at gmail.com  Sat Mar 19 11:21:17 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sat, 19 Mar 2011 11:21:17 +0000
Subject: [Open-bio-l] Fwd: OpenID enabled on most wikis
In-Reply-To: <1D6757C7-9A2D-4A73-89EA-72147D48A5FA@illinois.edu>
References: <7ACFE455-FC0B-46BC-8C5D-66317E2D9CCA@illinois.edu>
	<1D6757C7-9A2D-4A73-89EA-72147D48A5FA@illinois.edu>
Message-ID: <AANLkTi=ZkMiUv9RcM4q1gyhR+8wx8-OjyL8r7XrV0v9A@mail.gmail.com>

On 18 March 2011 16:03, Chris Fields <cjfields at illinois.edu> wrote:
> (Thinking about it, this probably should have gone to open-bio-l, so here it is)
>
> Begin forwarded message:
>
>> From: Chris Fields <cjfields at illinois.edu>
>> Date: March 18, 2011 11:02:55 AM CDT
>> To: Bioroot <root-l at open-bio.org>
>> Subject: OpenID enabled on most wikis
>>
>> Just to post that OpenID is now enabled on most wikis and is the only way new users can login to edit (the BioLib wiki is a notable exception, Pjotr wanted to manually approve new user accounts). ?The old login link is still present but new account creation is not allowed except by sysadmins.
>>
>> I already posted this to the news blogs, but I suppose we need to add something else to the wikis indicating this for new users?

Edit one of the system messages that appear on the login pages?

Is there a formal procedure for getting a particular extension or
other added to the obf wiki farm?


Cheers,
Dan.

>> chris
>
>
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>



From maisiliuma at gmail.com  Mon Mar  7 04:12:40 2011
From: maisiliuma at gmail.com (mais ar)
Date: Mon, 07 Mar 2011 04:12:40 -0000
Subject: [Open-bio-l] Bioinformatics
Message-ID: <AANLkTimMDPxGpxniXGnXxGH93L5T_EGhx6w3RfcVZe9c@mail.gmail.com>

Dear all,

      I'm having the promoter sequence. I want to know the domains,
transcriptors etc.. from the promoter Sequence.......... Any ideas,
suggestion pls......... Is there any softwares available.? Pls send me soon,
Thanks in advance.

Regards,
Uma.


From cjfields at illinois.edu  Tue Mar 29 20:33:27 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 29 Mar 2011 15:33:27 -0500
Subject: [Open-bio-l] Redmine and SSL
Message-ID: <3BDCA019-CCFD-4F47-8C90-57FD4E1684CF@illinois.edu>

All,

Just an update: since SSL authentication was added for redmine and everything has switched from http->https, in order for post-receive hooks from GitHub to work you will likely need to update the URL from http to https.  Just found this out myself testing bioperl commits with ref IDs in the commit messages.

chris


From rmb32 at cornell.edu  Tue Mar 29 21:20:41 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 29 Mar 2011 14:20:41 -0700
Subject: [Open-bio-l] Announcing OBF Summer of Code - please forward!
Message-ID: <4D924D29.3020707@cornell.edu>

Hi all,

Here's an advertising-ready announcement for OBF's Summer of Code, 
thanks to Christian Zmasek and Hilmar Lapp for their excellent writing.

Student applications are due April 8!  Please spread it widely, we need 
to reach lots of students with it!

Rob Buels
OBF GSoC 2011 Admin


============================================================

*** Please disseminate widely at your local institutions ***
*** including posting to message and job boards, so that ***
*** we reach as many students as possible.               ***

============================================================


OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011

Applications due 19:00 UTC, April 8, 2010.
http://www.open-bio.org/wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation Summer of Code program provides a 
unique opportunity for undergraduate, masters, and PhD students to 
obtain hands-on experience writing and extending open-source software 
for bioinformatics under the mentorship of experienced developers from 
around the world. The program is the participation of the Open 
Bioinformatics Foundation (OBF) as a mentoring organization in the 
Google Summer of Code(tm) (http://code.google.com/soc/).

Students successfully completing the 3 month program receive a $5,000 
USD stipend, and may work entirely from their home or home institution. 
  Participation is open to students from any country in the world except 
countries subject to US trade restrictions.  Each student will have at 
least one dedicated mentor to show them the ropes and help them complete 
their project.

The Open Bioinformatics Foundation is particularly seeking students 
interested in both bioinformatics (computational biology) and software 
development. Some initial project ideas are listed on the website. These 
range from Galaxy phylogenetics pipeline development in Biopython to 
lightweight sequence objects and lazy parsing in BioPerl, a DAS Server 
for large files on local filesystems, and mapping Java libraries to 
Perl/Ruby/Python using Biolib+SWIG+JNI.  All project ideas are flexible 
and many can be adjusted in scope to match the skills of the student. We 
also welcome and encourage students proposing their own project ideas; 
historically some of the most successful Summer of Code projects are 
ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website 
(http://socghop.appspot.com/), where you will also find GSoC program 
rules and eligibility requirements. The 12-day application period for 
students runs from Monday, March 28 through Friday, April 8th, 2011.

INQUIRIES:

We strongly encourage all interested students to get in touch with us 
with their ideas as early on as possible.  See the OBF GSoC page for 
contact details.

2011 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs